WorldWideScience

Sample records for revealing single emitter

  1. Nanodiamond Emitters of Single Photons

    Directory of Open Access Journals (Sweden)

    Vlasov I.I.

    2015-01-01

    Full Text Available Luminescence properties of single color centers were studied in nanodiamonds of different origin. It was found that single photon emitters could be realized even in molecularsized diamond (less than 2 nm capable of housing stable luminescent center “silicon-vacancy.” First results on incorporation of single-photon emitters based on luminescent nanodiamonds in plasmonic nanoantennas to enhance the photon count rate and directionality, diminish the fluorescence decay time, and provide polarization selectivity are presented.

  2. Coupling single emitters to quantum plasmonic circuits

    DEFF Research Database (Denmark)

    Huck, Alexander; Andersen, Ulrik Lund

    2016-01-01

    In recent years, the controlled coupling of single-photon emitters to propagating surface plasmons has been intensely studied, which is fueled by the prospect of a giant photonic nonlinearity on a nanoscaled platform. In this article, we will review the recent progress on coupling single emitters...

  3. Solid-state single-photon emitters

    Science.gov (United States)

    Aharonovich, Igor; Englund, Dirk; Toth, Milos

    2016-10-01

    Single-photon emitters play an important role in many leading quantum technologies. There is still no 'ideal' on-demand single-photon emitter, but a plethora of promising material systems have been developed, and several have transitioned from proof-of-concept to engineering efforts with steadily improving performance. Here, we review recent progress in the race towards true single-photon emitters required for a range of quantum information processing applications. We focus on solid-state systems including quantum dots, defects in solids, two-dimensional hosts and carbon nanotubes, as these are well positioned to benefit from recent breakthroughs in nanofabrication and materials growth techniques. We consider the main challenges and key advantages of each platform, with a focus on scalable on-chip integration and fabrication of identical sources on photonic circuits.

  4. Coupling single emitters to quantum plasmonic circuits

    Science.gov (United States)

    Huck, Alexander; Andersen, Ulrik L.

    2016-09-01

    In recent years, the controlled coupling of single-photon emitters to propagating surface plasmons has been intensely studied, which is fueled by the prospect of a giant photonic nonlinearity on a nanoscaled platform. In this article, we will review the recent progress on coupling single emitters to nanowires towards the construction of a new platform for strong light-matter interaction. The control over such a platform might open new doors for quantum information processing and quantum sensing at the nanoscale and for the study of fundamental physics in the ultrastrong coupling regime.

  5. Coupling single emitters to quantum plasmonic circuits

    CERN Document Server

    Huck, Alexander

    2016-01-01

    In recent years the controlled coupling of single photon emitters to propagating surface plasmons has been intensely studied, which is fueled by the prospect of a giant photonic non-linearity on a nano-scaled platform. In this article we will review the recent progress on coupling single emitters to nano-wires towards the construction of a new platform for strong light-matter interaction. The control over such a platform might open new doors for quantum information processing and quantum sensing at the nanoscale, and for the study of fundamental physics in the ultra-strong coupling regime.

  6. Correlated spontaneous emission of fluorescent emitters mediated by single plasmons

    CERN Document Server

    Bouchet, Dorian; Ithurria, Sandrine; Gulinatti, Angelo; Rech, Ivan; Carminati, Rémi; De Wilde, Yannick; Krachmalnicoff, Valentina

    2016-01-01

    Manipulating the spontaneous emission of a fluorescent emitter can be achieved by placing the emitter in a nanostructured environment. A privileged spot is occupied by plasmonic structures that provide a strong confinement of the electromagnetic field, which results in an enhancement of the emitter-environment interaction. While plasmonic nanostructures have been widely exploited to control the emission properties of single photon emitters, performing the coupling between quantum emitters with plasmons poses a huge challenge. In this Letter we report on a first crucial step towards this goal by the observation of correlated emission between a single CdSe/CdS/ZnS quantum dot exhibiting single photon statistics and a fluorescent nanobead located micrometers apart. This is accomplished by coupling both emitters to a silver nanowire. Single-plasmons are created on the latter from the quantum dot, and transfer energy to excite in turn the fluorescent nanobead.

  7. Spectral beam combining of multi-single emitters

    Science.gov (United States)

    Wang, Baohua; Guo, Weirong; Guo, Zhijie; Xu, Dan; Zhu, Jing; Zhang, Qiang; Yang, Thomas; Chen, Xiaohua

    2016-03-01

    Spectral beam combination expands the output power while keeps the beam quality of the combined beam almost the same as that of a single emitter. Spectral beam combination has been successfully achieved for high power fiber lasers, diode laser arrays and diode laser stacks. We have recently achieved the spectral beam combination of multiple single emitter diode lasers. Spatial beam combination and beam transformation are employed before beams from 25 single emitter diode lasers can be spectrally combined. An average output power about 220W, a spectral bandwidth less than 9 nm (95% energy), a beam quality similar to that of a single emitter and electro-optical conversion efficiency over 46% are achieved. In this paper, Rigorous Coupled Wave analysis is used to numerically evaluate the influence of emitter width, emitter pitch and focal length of transform lens on diffraction efficiency of the grating and spectral bandwidth. To assess the chance of catastrophic optical mirror damage (COMD), the optical power in the internal cavity of a free running emitter and the optical power in the grating external cavity of a wavelength locked emitter are theoretically analyzed. Advantages and disadvantages of spectral beam combination are concluded.

  8. Non-blinking single-photon emitters in silica

    NARCIS (Netherlands)

    Rabouw, F.T.; Cogan, N.M.B.; Berends, Anne; van der Stam, Ward; Vanmaekelbergh, Daniel|info:eu-repo/dai/nl/304829137; Koenderink, A.F.; Kraus, T.D.; de Mello-Donega, Celso|info:eu-repo/dai/nl/125593899

    2016-01-01

    Samples for single-emitter spectroscopy are usually prepared by spin-coating a dilute solution of emitters on a microscope cover slip of silicate based glass (such as quartz). Here, we show that both borosilicate glass and quartz contain intrinsic defect colour centres that fluoresce when excited at

  9. Nanostructure-induced distortion in single-emitter microscopy

    CERN Document Server

    Lim, Kangmook; Fourkas, John; Shapiro, Benjamin; Waks, Edo

    2016-01-01

    Single-emitter microscopy has emerged as a promising method of imaging nanostructures with nanoscale resolution. This technique uses the centroid position of an emitters far-field radiation pattern to infer its position to a precision that is far below the diffraction limit. However, nanostructures composed of high-dielectric materials such as noble metals can distort the far-field radiation pattern. Nanoparticles also exhibit a more complex range of distortions, because in addition to introducing a high dielectric surface, they also act as efficient scatterers. Thus, the distortion effects of nanoparticles in single-emitter microscopy remains poorly understood. Here we demonstrate that metallic nanoparticles can significantly distort the accuracy of single-emitter imaging at distances exceeding 300 nm. We use a single quantum dot to probe both the magnitude and the direction of the metallic nanoparticle-induced imaging distortion and show that the diffraction spot of the quantum dot can shift by more than 35...

  10. Vacuum Rabi spectra of a single quantum emitter

    CERN Document Server

    Ota, Yasutomo; Kumagai, Naoto; Iwamoto, Satoshi; Arakawa, Yasuhiko

    2015-01-01

    We report the observation of the vacuum Rabi splitting of a single quantum emitter by measuring its direct spontaneous emission into free space. We used a semiconductor quantum dot inside a photonic crystal nanocavity, in conjunction with an appropriate cavity design and filtering with a polarizer and an aperture, enabling the extraction of the inherently-weak emitter's signal. The emitter's vacuum Rabi spectra exhibit clear differences to those measured by detecting the cavity photon leakage. Moreover, we observed an asymmetric vacuum Rabi spectrum induced by interference between the emitter and cavity detection channels. Our observations lay the groundwork for accessing various cavity quantum electrodynamics phenomena that manifest themselves only in the emitter's direct spontaneous emission.

  11. Very bright, near-infrared single photon emitters in diamond

    Directory of Open Access Journals (Sweden)

    D. W. M. Lau

    2013-09-01

    Full Text Available We demonstrate activation of bright diamond single photon emitters in the near infrared range by thermal annealing alone, i.e., without ion implantation. The activation is crucially dependent on the annealing ambient. The activation of the single photon emitters is only observed when the sample is annealed in forming gas (4% H2 in Ar above temperatures of 1000 °C. By contrast, no emitters are activated by annealing in vacuum, oxygen, argon or deuterium. The emitters activated by annealing in forming gas exhibit very bright emission in the 730-760 nm wavelength range and have linewidths of ∼1.5-2.5 nm at room temperature.

  12. Localization of Narrowband Single Photon Emitters in Nanodiamonds.

    Science.gov (United States)

    Bray, Kerem; Sandstrom, Russell; Elbadawi, Christopher; Fischer, Martin; Schreck, Matthias; Shimoni, Olga; Lobo, Charlene; Toth, Milos; Aharonovich, Igor

    2016-03-23

    Diamond nanocrystals that host room temperature narrowband single photon emitters are highly sought after for applications in nanophotonics and bioimaging. However, current understanding of the origin of these emitters is extremely limited. In this work, we demonstrate that the narrowband emitters are point defects localized at extended morphological defects in individual nanodiamonds. In particular, we show that nanocrystals with defects such as twin boundaries and secondary nucleation sites exhibit narrowband emission that is absent from pristine individual nanocrystals grown under the same conditions. Critically, we prove that the narrowband emission lines vanish when extended defects are removed deterministically using highly localized electron beam induced etching. Our results enhance the current understanding of single photon emitters in diamond and are directly relevant to fabrication of novel quantum optics devices and sensors.

  13. Localization of narrowband single photon emitters in nanodiamonds

    CERN Document Server

    Bray, Kerem; Elbadawi, Christopher; Fischer, Martin; Schreck, Matthias; Shimoni, Olga; Lobo, Charlene; Toth, Milos; Aharonovich, Igor

    2016-01-01

    Diamond nanocrystals that host room temperature narrowband single photon emitters are highly sought after for applications in nanophotonics and bio-imaging. However, current understanding of the origin of these emitters is extremely limited. In this work we demonstrate that the narrowband emitters are point defects localized at extended morphological defects in individual nanodiamonds. In particular, we show that nanocrystals with defects such as twin boundaries and secondary nucleation sites exhibit narrowband emission that is absent from pristine individual nanocrystals grown under the same conditions. Critically, we prove that the narrowband emission lines vanish when extended defects are removed deterministically using highly localized electron beam induced etching. Our results enhance the current understanding of single photon emitters in diamond, and are directly relevant to fabrication of novel quantum optics devices and sensors.

  14. Wavelength locking of single emitters and multi-emitter modules: simulation and experiments

    Science.gov (United States)

    Yanson, Dan; Rappaport, Noam; Peleg, Ophir; Berk, Yuri; Dahan, Nir; Klumel, Genady; Baskin, Ilya; Levy, Moshe

    2016-03-01

    Wavelength-stabilized high-brightness single emitters are commonly used in fiber-coupled laser diode modules for pumping Yb-doped lasers at 976 nm, and Nd-doped ones at 808 nm. We investigate the spectral behavior of single emitters under wavelength-selective feedback from a volume Bragg (or hologram) grating (VBG) in a multi-emitter module. By integrating a full VBG model as a multi-layer thin film structure with commercial raytracing software, we simulated wavelength locking conditions as a function of beam divergence and angular alignment tolerances. Good correlation between the simulated VBG feedback strength and experimentally measured locking ranges, in both VBG misalignment angle and laser temperature, is demonstrated. The challenges of assembling multi-emitter modules based on beam-stacked optical architectures are specifically addressed, where the wavelength locking conditions must be achieved simultaneously with high fiber coupling efficiency for each emitter in the module. It is shown that angular misorientation between fast and slow-axis collimating optics can have a dramatic effect on the spectral and power performance of the module. We report the development of our NEON-S wavelength-stabilized fiber laser pump module, which uses a VBG to provide wavelength-selective optical feedback in the collimated portion of the beam. Powered by our purpose-developed high-brightness single emitters, the module delivers 47 W output at 11 A from an 0.15 NA fiber and a 0.3 nm linewidth at 976 nm. Preliminary wavelength-locking results at 808 nm are also presented.

  15. Nanostructure-Induced Distortion in Single-Emitter Microscopy

    Science.gov (United States)

    Lim, Kangmook; Ropp, Chad; Barik, Sabyasachi; Fourkas, John; Shapiro, Benjamin; Waks, Edo

    2016-09-01

    Single-emitter microscopy has emerged as a promising method of imaging nanostructures with nanoscale resolution. This technique uses the centroid position of an emitters far-field radiation pattern to infer its position to a precision that is far below the diffraction limit. However, nanostructures composed of high-dielectric materials such as noble metals can distort the far-field radiation pattern. Nanoparticles also exhibit a more complex range of distortions, because in addition to introducing a high dielectric surface, they also act as efficient scatterers. Thus, the distortion effects of nanoparticles in single-emitter microscopy remains poorly understood. Here we demonstrate that metallic nanoparticles can significantly distort the accuracy of single-emitter imaging at distances exceeding 300 nm. We use a single quantum dot to probe both the magnitude and the direction of the metallic nanoparticle-induced imaging distortion and show that the diffraction spot of the quantum dot can shift by more than 35 nm. The centroid position of the emitter generally shifts away from the nanoparticle position, in contradiction to the conventional wisdom that the nanoparticle is a scattering object that will pull in the diffraction spot of the emitter towards its center. These results suggest that dielectric distortion of the emission pattern dominates over scattering. We also show that by monitoring the distortion of the quantum dot diffraction spot we can obtain high-resolution spatial images of the nanoparticle, providing a new method for performing highly precise, sub-diffraction spatial imaging. These results provide a better understanding of the complex near-field coupling between emitters and nanostructures, and open up new opportunities to perform super-resolution microscopy with higher accuracy.

  16. High efficiency and stable white OLED using a single emitter

    Energy Technology Data Exchange (ETDEWEB)

    Li, Jian [Arizona State Univ., Tempe, AZ (United States). School of Mechanical, Aerospace, Chemical and Materials Engineering

    2016-01-18

    The ultimate objective of this project was to demonstrate an efficient and stable white OLED using a single emitter on a planar glass substrate. The focus of the project is on the development of efficient and stable square planar phosphorescent emitters and evaluation of such class of materials in the device settings. Key challenges included improving the emission efficiency of molecular dopants and excimers, controlling emission color of emitters and their excimers, and improving optical and electrical stability of emissive dopants. At the end of this research program, the PI has made enough progress to demonstrate the potential of excimer-based white OLED as a cost-effective solution for WOLED panel in the solid state lighting applications.

  17. Photon pair source via two coupling single quantum emitters

    Institute of Scientific and Technical Information of China (English)

    彭勇刚; 郑雨军

    2015-01-01

    We study the two coupling two-level single molecules driven by an external field as a photon pair source. The proba-bility of emitting two photons, P2, is employed to describe the photon pair source quality in a short time, and the correlation coefficient RAB is employed to describe the photon pair source quality in a long time limit. The results demonstrate that the coupling single quantum emitters can be considered as a stable photon pair source.

  18. Coherent single-photon absorption by single emitters coupled to one-dimensional nanophotonic waveguides

    DEFF Research Database (Denmark)

    Chen, Yuntian; Wubs, Martijn; Mørk, Jesper;

    2011-01-01

    We study the dynamics of single-photon absorption by a single emitter coupled to a one-dimensional waveguide that simultaneously provides channels for spontaneous emission (SE) decay and a channel for the input photon. We have developed a time-dependent theory that allows us to specify any input ...... can be improved by a further 4% by engineering the dispersion. Efficient single-photon absorption by a single emitter has potential applications in quantum communication and quantum computation....

  19. Electrically pumped single-defect light emitters in WSe$_2$

    CERN Document Server

    Schwarz, S; Withers, F; Maguire, J K; Foster, A P; Dufferwiel, S; Hague, L; Makhonin, M N; Wilson, L R; Geim, A K; Novoselov, K S; Tartakovskii, A I

    2016-01-01

    Recent developments in fabrication of van der Waals heterostructures enable new type of devices assembled by stacking atomically thin layers of two-dimensional materials. Using this approach, we fabricate light-emitting devices based on a monolayer WSe$_2$, and also comprising boron nitride tunnelling barriers and graphene electrodes, and observe sharp luminescence spectra from individual defects in WSe$_2$ under both optical and electrical excitation. This paves the way towards the realization of electrically-pumped quantum emitters in atomically thin semiconductors. In addition we demonstrate tuning by more than 1 meV of the emission energy of the defect luminescence by applying a vertical electric field. This provides an estimate of the permanent electric dipole created by the corresponding electron-hole pair. The light-emitting devices investigated in our work can be assembled on a variety of substrates enabling a route to integration of electrically pumped single quantum emitters with existing technologi...

  20. Operating single quantum emitters with a compact Stirling cryocooler

    Energy Technology Data Exchange (ETDEWEB)

    Schlehahn, A.; Krüger, L.; Gschrey, M.; Schulze, J.-H.; Rodt, S.; Strittmatter, A.; Heindel, T., E-mail: tobias.heindel@tu-berlin.de; Reitzenstein, S. [Institute of Solid State Physics, Technische Universität Berlin, 10623 Berlin (Germany)

    2015-01-15

    The development of an easy-to-operate light source emitting single photons has become a major driving force in the emerging field of quantum information technology. Here, we report on the application of a compact and user-friendly Stirling cryocooler in the field of nanophotonics. The Stirling cryocooler is used to operate a single quantum emitter constituted of a semiconductor quantum dot (QD) at a base temperature below 30 K. Proper vibration decoupling of the cryocooler and its surrounding enables free-space micro-photoluminescence spectroscopy to identify and analyze different charge-carrier states within a single quantum dot. As an exemplary application in quantum optics, we perform a Hanbury-Brown and Twiss experiment demonstrating a strong suppression of multi-photon emission events with g{sup (2)}(0) < 0.04 from this Stirling-cooled single quantum emitter under continuous wave excitation. Comparative experiments performed on the same quantum dot in a liquid helium (LHe)-flow cryostat show almost identical values of g{sup (2)}(0) for both configurations at a given temperature. The results of this proof of principle experiment demonstrate that low-vibration Stirling cryocoolers that have so far been considered exotic to the field of nanophotonics are an attractive alternative to expensive closed-cycle cryostats or LHe-flow cryostats, which could pave the way for the development of high-quality table-top non-classical light sources.

  1. Operating single quantum emitters with a compact Stirling cryocooler.

    Science.gov (United States)

    Schlehahn, A; Krüger, L; Gschrey, M; Schulze, J-H; Rodt, S; Strittmatter, A; Heindel, T; Reitzenstein, S

    2015-01-01

    The development of an easy-to-operate light source emitting single photons has become a major driving force in the emerging field of quantum information technology. Here, we report on the application of a compact and user-friendly Stirling cryocooler in the field of nanophotonics. The Stirling cryocooler is used to operate a single quantum emitter constituted of a semiconductor quantum dot (QD) at a base temperature below 30 K. Proper vibration decoupling of the cryocooler and its surrounding enables free-space micro-photoluminescence spectroscopy to identify and analyze different charge-carrier states within a single quantum dot. As an exemplary application in quantum optics, we perform a Hanbury-Brown and Twiss experiment demonstrating a strong suppression of multi-photon emission events with g((2))(0) Stirling-cooled single quantum emitter under continuous wave excitation. Comparative experiments performed on the same quantum dot in a liquid helium (LHe)-flow cryostat show almost identical values of g((2))(0) for both configurations at a given temperature. The results of this proof of principle experiment demonstrate that low-vibration Stirling cryocoolers that have so far been considered exotic to the field of nanophotonics are an attractive alternative to expensive closed-cycle cryostats or LHe-flow cryostats, which could pave the way for the development of high-quality table-top non-classical light sources.

  2. Operating single quantum emitters with a compact Stirling cryocooler

    Science.gov (United States)

    Schlehahn, A.; Krüger, L.; Gschrey, M.; Schulze, J.-H.; Rodt, S.; Strittmatter, A.; Heindel, T.; Reitzenstein, S.

    2015-01-01

    The development of an easy-to-operate light source emitting single photons has become a major driving force in the emerging field of quantum information technology. Here, we report on the application of a compact and user-friendly Stirling cryocooler in the field of nanophotonics. The Stirling cryocooler is used to operate a single quantum emitter constituted of a semiconductor quantum dot (QD) at a base temperature below 30 K. Proper vibration decoupling of the cryocooler and its surrounding enables free-space micro-photoluminescence spectroscopy to identify and analyze different charge-carrier states within a single quantum dot. As an exemplary application in quantum optics, we perform a Hanbury-Brown and Twiss experiment demonstrating a strong suppression of multi-photon emission events with g(2)(0) < 0.04 from this Stirling-cooled single quantum emitter under continuous wave excitation. Comparative experiments performed on the same quantum dot in a liquid helium (LHe)-flow cryostat show almost identical values of g(2)(0) for both configurations at a given temperature. The results of this proof of principle experiment demonstrate that low-vibration Stirling cryocoolers that have so far been considered exotic to the field of nanophotonics are an attractive alternative to expensive closed-cycle cryostats or LHe-flow cryostats, which could pave the way for the development of high-quality table-top non-classical light sources.

  3. Single-bunch emittance dilution in the perfect ILC main linac

    Institute of Scientific and Technical Information of China (English)

    WANG Dou; GAO Jie

    2011-01-01

    In the ILC(International Linear Collider)main linac, low emittance preservation is the most important issue for beam dynamics study. As the main sources of emittance dilution, the dispersive and wakefield effects were studied in this paper. The theoretical calculations and numerical simulations of these two effects on single-bunch emittance dilution, without any misalignment errors, are presented in detail.

  4. 99% efficiency in collecting photons from a single emitter

    CERN Document Server

    Chen, Xue-Wen; Sandoghdar, Vahid

    2011-01-01

    In Nature Photonics 5, 166 (2011), we reported on a planar dielectric antenna that achieved 96% efficiency in collecting the photons emitted by a single molecule. In that work the transition dipole moment of the molecule was set perpendicular to the antenna plane. Here, we present an extension of that scheme that reaches collection efficiencies beyond 99% for emitters with arbitrarily oriented dipole moments. Our work opens important doors in a wide range of contexts including quantum optics, quantum metrology, nano-analytics, and biophysics. In particular, we provide antenna parameters to realize ultrabright single-photon sources in high-index materials such as semiconductor quantum dots and color centers in diamond, as well as sensitive detection of single molecules in nanofluidic devices.

  5. Vacuum Rabi splitting in a plasmonic cavity at the single quantum emitter limit

    CERN Document Server

    Santhosh, Kotni; Chuntonov, Lev; Haran, Gilad

    2015-01-01

    The strong interaction of individual quantum emitters with resonant cavities is of fundamental interest for understanding light matter interactions, as well as for quantum information processing and quantum communication applications. Plasmonic cavities hold the promise of attaining the strong coupling regime even under ambient conditions and within subdiffraction volumes. Recent experiments revealed strong coupling between individual plasmonic structures and multiple organic molecules, but so far strong coupling at the limit of a single quantum emitter has not been reported. Here we demonstrate vacuum Rabi splitting, a manifestation of strong coupling, using silver bowtie plasmonic cavities loaded with semiconductor quantum dots (QDs). A transparency dip is observed in the scattering spectra of individual bowties with one to a few QDs in their gaps. Rabi splitting values as high as 180 meV are registered with a single QD. These observations are verified by polarization-dependent experiments and validated by ...

  6. Vacuum Rabi splitting in a plasmonic cavity at the single quantum emitter limit.

    Science.gov (United States)

    Santhosh, Kotni; Bitton, Ora; Chuntonov, Lev; Haran, Gilad

    2016-06-13

    The strong interaction of individual quantum emitters with resonant cavities is of fundamental interest for understanding light-matter interactions. Plasmonic cavities hold the promise of attaining the strong coupling regime even under ambient conditions and within subdiffraction volumes. Recent experiments revealed strong coupling between individual plasmonic structures and multiple organic molecules; however, strong coupling at the limit of a single quantum emitter has not been reported so far. Here we demonstrate vacuum Rabi splitting, a manifestation of strong coupling, using silver bowtie plasmonic cavities loaded with semiconductor quantum dots (QDs). A transparency dip is observed in the scattering spectra of individual bowties with one to a few QDs, which are directly counted in their gaps. A coupling rate as high as 120 meV is registered even with a single QD, placing the bowtie-QD constructs close to the strong coupling regime. These observations are verified by polarization-dependent experiments and validated by electromagnetic calculations.

  7. Bright and stable visible-spectrum single photon emitter in silicon carbide

    CERN Document Server

    Lienhard, Benjamin; Mouradian, Sara; Dolde, Florian; Tran, Toan Trong; Aharonovich, Igor; Englund, Dirk R

    2016-01-01

    Single photon sources are of paramount importance in quantum communication, quantum computation, and quantum metrology. In particular, there is great interest to realize scalable solid state platforms that can emit triggered photons on demand to achieve scalable nanophotonic networks. We report on a visible-spectrum single photon emitter in 4H-silicon carbide (SiC). The emitter is photostable at room- and low-temperature enabling photon counts per second (cps) in excess of 2$\\times$10$^6$ from unpatterned, bulk SiC. It exists in two orthogonally polarized states, which have parallel absorption and emission dipole orientations. Low temperature measurements reveal a narrow zero phonon line (linewidth $30~$% of the total photoluminescence spectrum.

  8. Electrically pumped single-defect light emitters in WSe2

    Science.gov (United States)

    Schwarz, S.; Kozikov, A.; Withers, F.; Maguire, J. K.; Foster, A. P.; Dufferwiel, S.; Hague, L.; Makhonin, M. N.; Wilson, L. R.; Geim, A. K.; Novoselov, K. S.; Tartakovskii, A. I.

    2016-06-01

    Recent developments in fabrication of van der Waals heterostructures enable new type of devices assembled by stacking atomically thin layers of two-dimensional materials. Using this approach, we fabricate light-emitting devices based on a monolayer WSe2, and also comprising boron nitride tunnelling barriers and graphene electrodes, and observe sharp luminescence spectra from individual defects in WSe2 under both optical and electrical excitation. This paves the way towards the realisation of electrically-pumped quantum emitters in atomically thin semiconductors. In addition we demonstrate tuning by more than 1 meV of the emission energy of the defect luminescence by applying a vertical electric field. This provides an estimate of the permanent electric dipole created by the corresponding electron-hole pair. The light-emitting devices investigated in our work can be assembled on a variety of substrates enabling a route to integration of electrically pumped single quantum emitters with existing technologies in nano-photonics and optoelectronics.

  9. Reconstruction of the environmental correlation function from single emitter photon statistics: a non-Markovian approach

    CERN Document Server

    Shikerman, Faina; Pe'er, Avi

    2012-01-01

    We consider the two-level system approximation of a single emitter driven by a continuous laser pump and simultaneously coupled to the electromagnetic vacuum and to a thermal reservoir beyond the Markovian approximation. We discuss the connection between a rigorous microscopic theory and the phenomenological spectral diffusion approach, used to model the interaction of the emitter with the thermal bath, and obtained analytic expressions relating the thermal correlation function to the single emitter photon statistics.

  10. Nonclassical light from a large number of independent single-photon emitters

    CERN Document Server

    Lachman, Lukáš; Filip, Radim

    2016-01-01

    Nonclassical quantum effects gradually reach domains of physics of large systems previously considered as purely classical. We derive a hierarchy of operational criteria suitable for a reliable detection of nonclassicality of light from an arbitrarily large ensemble of independent single-photon emitters. We show, that such large ensemble can always emit nonclassical light without any phase reference and under realistic experimental conditions including incoherent background noise. The nonclassical light from the large ensemble of the emitters can be witnessed much better than light coming from a single or a few emitters.

  11. Describing a Laser Diode Emulation Tool Using Single Emitter Simulation Results

    Directory of Open Access Journals (Sweden)

    C.K. Amuzuvi

    2013-02-01

    Full Text Available This study describes and explores the use of a laser diode simulation tool at the single emitter level of operation and how they can be degraded. A test of the simulation tool is implemented to complement the by-emitter degradation analysis of high power laser diodes. The simulation tool is called Speclase, designed for the simulation of single emitters. Tests were performed using a 975 nm narrow-angle (<1º tapered laser structure from Alcatel Thales III-V Lab with front and rear facet reflectivities of 3 and 90%, respectively. The tool worked for both the constant current and power modes of operation. Simulation results were obtained for both constant QW trap density, based on the maximum QW temperature and variable QW trap density generation due to local heating. Single emitter degradation results are obtained using the Arrhenius equation to compare the rate of degradation between the constant and variable QW trap densities.

  12. Single shot 3 GeV electron transverse emittance with a pepper-pot

    Science.gov (United States)

    Thomas, Cyrille; Delerue, Nicolas; Bartolini, Riccardo

    2013-11-01

    We present the first measurement of the transverse emittance of an electron bunch at 3 GeV using the pepper-pot technique. The measurements presented in this paper demonstrate the possibility to use such a method for single shot emittance measurement of high energy particles. This measurement presents also the experimental verification of a previous theoretical study, which was predicting in which condition such a measurement can be done. The method may present some technical limitations which are discussed in view of the application to future very small emittance multi-GeV particle accelerators.

  13. Coherent interaction of a metallic structure with a single quantum emitter: from super absorption to cloaking

    CERN Document Server

    Chen, Xue-Wen; Agio, Mario

    2012-01-01

    We provide a general theoretical platform based on quantized radiation in absorptive and inhomogeneous media for investigating the coherent interaction of light with metallic structures in the immediate vicinity of quantum emitters. In the case of a very small metallic cluster, we demonstrate extreme regimes where a single emitter can either counteract or enhance particle absorption by three orders of magnitude. For larger structures, we show that an emitter can eliminate both scattering and absorption and cloak a plasmonic antenna. We provide physical interpretations of our results and discuss their applications in active metamaterials and quantum plasmonics.

  14. Wiring up pre-characterized single-photon emitters by laser lithography

    Science.gov (United States)

    Shi, Q.; Sontheimer, B.; Nikolay, N.; Schell, A. W.; Fischer, J.; Naber, A.; Benson, O.; Wegener, M.

    2016-08-01

    Future quantum optical chips will likely be hybrid in nature and include many single-photon emitters, waveguides, filters, as well as single-photon detectors. Here, we introduce a scalable optical localization-selection-lithography procedure for wiring up a large number of single-photon emitters via polymeric photonic wire bonds in three dimensions. First, we localize and characterize nitrogen vacancies in nanodiamonds inside a solid photoresist exhibiting low background fluorescence. Next, without intermediate steps and using the same optical instrument, we perform aligned three-dimensional laser lithography. As a proof of concept, we design, fabricate, and characterize three-dimensional functional waveguide elements on an optical chip. Each element consists of one single-photon emitter centered in a crossed-arc waveguide configuration, allowing for integrated optical excitation and efficient background suppression at the same time.

  15. Simultaneous measurement of position and color of single fluorescent emitters using diffractive optics

    NARCIS (Netherlands)

    Broeken, J.; Rieger, B.; Stallinga, S.

    2014-01-01

    We propose a method for simultaneously measuring the position and emission color of single fluorescent emitters based on the use of a large pitch diffraction grating in the emission light path. The grating produces satellite spots adjacent to the main spot; the relative distance between the spots is

  16. Large suppression of quantum fluctuations of light from a single emitter by an optical nanostructure

    CERN Document Server

    Cano, Diego Martín; Murr, Karim; Agio, Mario

    2014-01-01

    We investigate the reduction of the electromagnetic field fluctuations in resonance fluorescence from a single emitter coupled to an optical nanostructure. We find that such hybrid system can lead to the creation of squeezed states of light, with quantum fluctuations significantly below the shot noise level. Moreover, the physical conditions for achieving squeezing are strongly relaxed with respect to an emitter in free space. A high degree of control over squeezed light is feasible both in the far and near fields, opening the pathway to its manipulation and applications on the nanoscale with state-of-the-art setups.

  17. Moving scanning emitter tracking by a single observer using time of interception: Observability analysis and algorithm

    Directory of Open Access Journals (Sweden)

    Yifei ZHANG

    2017-06-01

    Full Text Available The target motion analysis (TMA for a moving scanning emitter with known fixed scan rate by a single observer using the time of interception (TOI measurements only is investigated in this paper. By transforming the TOI of multiple scan cycles into the direction difference of arrival (DDOA model, the observability analysis for the TMA problem is performed. Some necessary conditions for uniquely identifying the scanning emitter trajectory are obtained. This paper also proposes a weighted instrumental variable (WIV estimator for the scanning emitter TMA, which does not require any initial solution guess and is closed-form and computationally attractive. More importantly, simulations show that the proposed algorithm can provide estimation mean square error close to the Cramer-Rao lower bound (CRLB at moderate noise levels with significantly lower estimation bias than the conventional pseudo-linear least square (PLS estimator.

  18. Single light emitters in the confinement of polymers

    OpenAIRE

    Tomczak, Nikodem

    2005-01-01

    This thesis presents developments in the field of nanoscale probing of polymers. New experimental methods based on single molecule fluorescence detection were developed and applied to polymer studies. Localization of, and communication with individual fluorescent molecules embedded in a glassy polymer or immersed in a polymer melt have been realized by using various, optical techniques e.g. Scanning Confocal Microscopy and Wide-Field Microscopy. Location of single molecules as well as their o...

  19. Single light emitters in the confinement of polymers

    NARCIS (Netherlands)

    Tomczak, Nikodem

    2005-01-01

    This thesis presents developments in the field of nanoscale probing of polymers. New experimental methods based on single molecule fluorescence detection were developed and applied to polymer studies. Localization of, and communication with individual fluorescent molecules embedded in a glassy polym

  20. Engineering near-infrared single-photon emitters with optically active spins in ultrapure silicon carbide

    Science.gov (United States)

    Fuchs, F.; Stender, B.; Trupke, M.; Simin, D.; Pflaum, J.; Dyakonov, V.; Astakhov, G. V.

    2015-07-01

    Vacancy-related centres in silicon carbide are attracting growing attention because of their appealing optical and spin properties. These atomic-scale defects can be created using electron or neutron irradiation; however, their precise engineering has not been demonstrated yet. Here, silicon vacancies are generated in a nuclear reactor and their density is controlled over eight orders of magnitude within an accuracy down to a single vacancy level. An isolated silicon vacancy serves as a near-infrared photostable single-photon emitter, operating even at room temperature. The vacancy spins can be manipulated using an optically detected magnetic resonance technique, and we determine the transition rates and absorption cross-section, describing the intensity-dependent photophysics of these emitters. The on-demand engineering of optically active spins in technologically friendly materials is a crucial step toward implementation of both maser amplifiers, requiring high-density spin ensembles, and qubits based on single spins.

  1. Ordered arrays of InGaN/GaN dot-in-a-wire nanostructures as single photon emitters

    Science.gov (United States)

    Lazić, Snežana; Chernysheva, Ekaterina; Gačević, Žarko; García-Lepetit, Noemi; van der Meulen, Herko P.; Müller, Marcus; Bertram, Frank; Veit, Peter; Christen, Jürgen; Torres-Pardo, Almudena; González Calbet, José M.; Calleja, Enrique; Calleja, José M.

    2015-03-01

    The realization of reliable single photon emitters operating at high temperature and located at predetermined positions still presents a major challenge for the development of solid-state systems for quantum light applications. We demonstrate single-photon emission from two-dimensional ordered arrays of GaN nanowires containing InGaN nanodisks. The structures were fabricated by molecular beam epitaxy on (0001) GaN-on-sapphire templates patterned with nanohole masks prepared by colloidal lithography. Low-temperature cathodoluminescence measurements reveal the spatial distribution of light emitted from a single nanowire heterostructure. The emission originating from the topmost part of the InGaN regions covers the blue-to-green spectral range and shows intense and narrow quantum dot-like photoluminescence lines. These lines exhibit an average linear polarization ratio of 92%. Photon correlation measurements show photon antibunching with a g(2)(0) values well below the 0.5 threshold for single photon emission. The antibunching rate increases linearly with the optical excitation power, extrapolating to the exciton decay rate of ~1 ns-1 at vanishing pump power. This value is comparable with the exciton lifetime measured by time-resolved photoluminescence. Fast and efficient single photon emitters with controlled spatial position and strong linear polarization are an important step towards high-speed on-chip quantum information management.

  2. High quality GaAs single photon emitters on Si substrate

    Energy Technology Data Exchange (ETDEWEB)

    Bietti, S.; Sanguinetti, S. [Dipartimento di Scienza dei Materiali and L-NESS, Università, di Milano Bicocca, Via Cozzi 53,I-20125 Milano (Italy); Cavigli, L.; Accanto, N.; Vinattieri, A. [Dipartimento di Fisica e Astronomia, LENS and CNISM, Università, di Firenze, Via Sansone 1, I-50019 Firenze (Italy); Minari, S.; Abbarchi, M. [Dipartimento di Fisica e Astronomia, LENS and CNISM, Universita di Firenze, Via Sansone 1, I-50019 Firenze (Italy); Isella, G. [Dipartimento di Fisica and L-NESS, Politecnico di Milano, Via Anzani 42, 22100 Como (Italy); Frigeri, C. [CNR-IMEM Institute, Parco Area delle Scienze 31/A, 43100 Parma (Italy); Gurioli, M. [Dipartimento di Fisica e Astronomia, LENS and CNISM, Universita, di Firenze, Via Sansone 1, I-50019 Firenze (Italy)

    2013-12-04

    We describe a method for the direct epitaxial growth of a single photon emitter, based on GaAs quantum dots fabricated by droplet epitaxy, working at liquid nitrogen temperatures on Si substrates. The achievement of quantum photon statistics up to T=80 K is directly proved by antibunching in the second order correlation function as measured with a H anbury Brown and Twiss interferometer.

  3. Bow-tie optical antenna probes for single-emitter scanning near-field optical microscopy

    Energy Technology Data Exchange (ETDEWEB)

    Farahani, Javad N [Nano-Optics Group, National Center of Competence for Research in Nanoscale Science, Institute of Physics, University of Basel, Klingelbergstrasse 82, CH-4056 Basel (Switzerland); Eisler, Hans-Juergen [Nano-Optics Group, National Center of Competence for Research in Nanoscale Science, Institute of Physics, University of Basel, Klingelbergstrasse 82, CH-4056 Basel (Switzerland); Pohl, Dieter W [Nano-Optics Group, National Center of Competence for Research in Nanoscale Science, Institute of Physics, University of Basel, Klingelbergstrasse 82, CH-4056 Basel (Switzerland); Pavius, Michael [Center of MicroNanoTechnology (CMI), Ecole Polytechnique Federale de Lausanne (EPFL), CH-1015 Lausanne (Switzerland); Flueckiger, Philippe [Center of MicroNanoTechnology (CMI), Ecole Polytechnique Federale de Lausanne (EPFL), CH-1015 Lausanne (Switzerland); Gasser, Philippe [EMPA, Swiss Federal Laboratories for Materials Testing and Research, Electronics/Metrology Laboratory, Ueberlandstrasse 129, CH-8600 Duebendorf (Switzerland); Hecht, Bert [Nano-Optics Group, National Center of Competence for Research in Nanoscale Science, Institute of Physics, University of Basel, Klingelbergstrasse 82, CH-4056 Basel (Switzerland)

    2007-03-28

    A method for the fabrication of bow-tie optical antennas at the apex of pyramidal Si{sub 3}N{sub 4} atomic force microscopy tips is described. We demonstrate that these novel optical probes are capable of sub-wavelength imaging of single quantum dots at room temperature. The enhanced and confined optical near-field at the antenna feed gap leads to locally enhanced photoluminescence (PL) of single quantum dots. Photoluminescence quenching due to the proximity of metal is found to be insignificant. The method holds promise for single quantum emitter imaging and spectroscopy at spatial resolution limited by the engineered antenna gap width exclusively.

  4. Single photon transport in two waveguides chirally coupled by a quantum emitter.

    Science.gov (United States)

    Cheng, Mu-Tian; Ma, Xiao-San; Zhang, Jia-Yan; Wang, Bing

    2016-08-22

    We investigate single photon transport in two waveguides coupled to a two-level quantum emitter (QE). With the deduced analytical scattering amplitudes, we show that under condition of the chiral coupling between the QE and the photon in the two waveguides, the QE can play the role of ideal quantum router to redirect a single photon incident from one waveguide into the other waveguide with a probability of 100% in the ideal condition. The influences of cross coupling between two waveguides and dissipations on the routing are also shown.

  5. Uncovering Single-Molecule Photophysical Heterogeneity of Bright, Thermally Activated Delayed Fluorescence Emitters Dispersed in Glassy Hosts.

    Science.gov (United States)

    Noriega, Rodrigo; Barnard, Edward S; Ursprung, Benedikt; Cotts, Benjamin L; Penwell, Samuel B; Schuck, P James; Ginsberg, Naomi S

    2016-10-04

    Recently developed all-organic emitters used in display applications achieve high brightness by harvesting triplet populations via thermally activated delayed fluorescence. The photophysical properties of these emitters therefore involve new inherent complexities and are strongly affected by interactions with their host material in the solid state. Ensemble measurements occlude the molecular details of how host-guest interactions determine fundamental properties such as the essential balance of singlet oscillator strength and triplet harvesting. Therefore, using time-resolved fluorescence spectroscopy, we interrogate these emitters at the single-molecule level and compare their properties in two distinct glassy polymer hosts. We find that nonbonding interactions with aromatic moieties in the host appear to mediate the molecular configurations of the emitters, but also promote nonradiative quenching pathways. We also find substantial heterogeneity in the time-resolved photoluminescence of these emitters, which is dominated by static disorder in the polymer. Finally, since singlet-triplet cycling underpins the mechanism for increased brightness, we present the first room-temperature measurement of singlet-triplet equilibration dynamics in this family of emitters. Our observations present a molecular-scale interrogation of host-guest interactions in a disordered film, with implications for highly efficient organic light-emitting devices. Combining a single-molecule experimental technique with an emitter that is sensitive to triplet dynamics, yet read out via fluorescence, should also provide a complementary approach to performing fundamental studies of glassy materials over a large dynamic range of time scales.

  6. Scalable Focused Ion Beam Creation of Nearly Lifetime-Limited Single Quantum Emitters in Diamond Nanostructures

    CERN Document Server

    Schröder, Tim; Walsh, Michael; Li, Luozhou; Zheng, Jiabao; Schukraft, Marco; Pacheco, Jose L; Camacho, Ryan M; Bielejec, Edward S; Sipahigil, Alp; Evans, Ruffin E; Sukachev, Denis D; Nguyen, Christian T; Lukin, Mikhail D; Englund, Dirk

    2016-01-01

    The controlled creation of defect center---nanocavity systems is one of the outstanding challenges for efficiently interfacing spin quantum memories with photons for photon-based entanglement operations in a quantum network. Here, we demonstrate direct, maskless creation of atom-like single silicon-vacancy (SiV) centers in diamond nanostructures via focused ion beam implantation with $\\sim 32$ nm lateral precision and $< 50$ nm positioning accuracy relative to a nanocavity. Moreover, we determine the Si+ ion to SiV center conversion yield to $\\sim 2.5\\%$ and observe a 10-fold conversion yield increase by additional electron irradiation. We extract inhomogeneously broadened ensemble emission linewidths of $\\sim 51$ GHz, and close to lifetime-limited single-emitter transition linewidths down to $126 \\pm13$ MHz corresponding to $\\sim 1.4$-times the natural linewidth. This demonstration of deterministic creation of optically coherent solid-state single quantum systems is an important step towards development o...

  7. Probing the local density of states in three dimensions with a scanning single quantum emitter

    CERN Document Server

    Schell, Andreas W; Benson, Oliver

    2013-01-01

    Their intrinsic properties render single quantum systems as ideal tools for quantum enhanced sensing and microscopy. As an additional benefit, their size is typically on an atomic scale which enables sensing with very high spatial resolution. Here, we report on utilizing a single nitrogen vacancy center in nanodiamond for performing three-dimensional scanning-probe fluorescence lifetime imaging microscopy. By measuring changes of the single emitter's lifetime information on the local density of optical states is acquired at the nanoscale. This technique to gather information on the local density of optical states is important for the understanding of fundamental quantum optical processes as well as for the engineering of novel photonic and plasmonic devices.

  8. Investigating a Hypothetical Semiconductor Laser Bar with a Damaged Single Emitter Using a Laser Diode Simulation/Emulation Tool

    Directory of Open Access Journals (Sweden)

    C.K. Amuzuvi

    2014-02-01

    Full Text Available This study demonstrates the use of Barlase, a semiconductor laser diode emulation tool, to emulate the by-emitter degradation of high power semiconductor laser diodes.Barlase is software that uses a LabView control interface. In this study, a hypothetical laser diode bar (multiple emitters was used to investigate a damaged single emitter randomly located in the bar and its behavior analyzed within the bar. It should however, be noted that, this scenario is valid for devices at the start of the aging process only. When all other relevant effects that affect the performance of laser diodes bars are allowed to interact over time, high levels of defects can also play important role in the degradation process. The results of this simulation scenario show the successful implementation of Barlase in the by-emitter analysis of laser diodes.

  9. Irving Langmuir Prize Talk: Single-Molecule Fluorescence Imaging: Nanoscale Emitters with Photoinduced Switching Enable Superresolution.

    Science.gov (United States)

    Moerner, W. E.

    2009-03-01

    In the two decades since the first optical detection and spectroscopy of a single molecule in a solid (Phys. Rev. Lett. 62, 2535 (1989)), much has been learned about the ability of single molecules to probe local nanoenvironments and individual behavior in biological and nonbiological materials in the absence of ensemble averaging that can obscure heterogeneity. The early years concentrated on high-resolution spectroscopy in solids, which provided observations of lifetime-limited spectra, optical saturation, spectral diffusion, optical switching, vibrational spectra, and magnetic resonance of a single molecular spin. In the mid-1990's, much of the field moved to room temperature, where a wide variety of biophysical effects were subsequently explored, but it is worth noting that several features from the low-temperature studies have analogs at high temperature. For example, in our first studies of yellow-emitting variants of green fluorescent protein (EYFP) in the water-filled pores of a gel (Nature 388, 355 (1997)), optically induced switching of the emission was observed, a room-temperature analog of the earlier low-temperature behavior. Because each single fluorophore acts a light source roughly 1 nm in size, microscopic imaging of individual fluorophores leads naturally to superlocalization, or determination of the position of the molecule with precision beyond the optical diffraction limit, simply by digitization of the point-spread function from the single emitter. Recent work has allowed measurement of the shape of single filaments in a living cell simply by allowing a single molecule to move through the filament (PNAS 103, 10929 (2006)). The additional use of photoinduced control of single-molecule emission allows imaging beyond the diffraction limit (superresolution) by several novel approaches proposed by different researchers. For example, using photoswitchable EYFP, a novel protein superstructure can now be directly imaged in a living bacterial cell at

  10. Surface Analysis of LaB6 Single Crystal Thermionic Emitters

    Science.gov (United States)

    Nakazawa, Masatoshi; Futamoto, Masaaki; Hosoki, Shigeyuki; Usami, Katuhisa

    1980-07-01

    Surface analysis of heated LaB6 thermionic emitter is made by means of Auger electron spectroscopy. Changes in surface state with changing emitter temperature and ambient oxygen pressure are investigated. The emitter temperature is varied from room temperature to 1700°C, and the oxygen pressure from 1× 10-5 Pa to 7× 10-3 Pa. With the increase of temperature the emitter surface passes through four states depending on oxygen pressure, before it reaches a clean state. Among them a state is particularly noteworthy that the emitter surface is covered with a layer of lanthanum oxide just before assuming the clean surface state. A surface state diagram is shown. The optimum conditions of emitter temperature and oxygen gas pressure to exhibit high emission properties are described.

  11. Single-bunch emittance dilution in the perfect ILC main linac

    Institute of Scientific and Technical Information of China (English)

    王逗; 高杰

    2011-01-01

    In the ILC (International Linear Collider) main linac, low emittance preservation is the most important issue for beam dynamics study. As the main sources of emittance dilution, the dispersive and wakefield effects were studied in this paper. The theoreti

  12. A state space based approach to localizing single molecules from multi-emitter images.

    Science.gov (United States)

    Vahid, Milad R; Chao, Jerry; Ward, E Sally; Ober, Raimund J

    2017-01-28

    Single molecule super-resolution microscopy is a powerful tool that enables imaging at sub-diffraction-limit resolution. In this technique, subsets of stochastically photoactivated fluorophores are imaged over a sequence of frames and accurately localized, and the estimated locations are used to construct a high-resolution image of the cellular structures labeled by the fluorophores. Available localization methods typically first determine the regions of the image that contain emitting fluorophores through a process referred to as detection. Then, the locations of the fluorophores are estimated accurately in an estimation step. We propose a novel localization method which combines the detection and estimation steps. The method models the given image as the frequency response of a multi-order system obtained with a balanced state space realization algorithm based on the singular value decomposition of a Hankel matrix, and determines the locations of intensity peaks in the image as the pole locations of the resulting system. The locations of the most significant peaks correspond to the locations of single molecules in the original image. Although the accuracy of the location estimates is reasonably good, we demonstrate that, by using the estimates as the initial conditions for a maximum likelihood estimator, refined estimates can be obtained that have a standard deviation close to the Cramér-Rao lower bound-based limit of accuracy. We validate our method using both simulated and experimental multi-emitter images.

  13. A stable, single-photon emitter in a thin organic crystal for application to quantum-photonic devices

    CERN Document Server

    Polisseni, Claudio; Boissier, Sebastien; Grandi, Samuele; Clark, Alex S; Hinds, E A

    2016-01-01

    Single organic molecules offer great promise as bright, reliable sources of identical single photons on demand, capable of integration into solid-state devices. It has been proposed that such molecules in a crystalline organic matrix might be placed close to an optical waveguide for this purpose, but so far there have been no demonstrations of sufficiently thin crystals, with a controlled concentration of suitable dopant molecules. Here we present a method for growing very thin anthracene crystals from super-saturated vapour, which produces crystals of extreme flatness and controlled thickness. We show how this crystal can be doped with a widely adjustable concentration of dibenzoterrylene (DBT) molecules and we examine the optical properties of these molecules to demonstrate their suitability as quantum emitters in nanophotonic devices. Our measurements show that the molecules are available in the crystal as single quantum emitters, with a well-defined polarisation relative to the crystal axes, making them a...

  14. Advances in 808nm high power diode laser bars and single emitters

    Science.gov (United States)

    Morales, J.; Lehkonen, S.; Liu, G.; Schleuning, D.; Acklin, B.

    2016-03-01

    Key applications for 780-830nm high power diode lasers include the pumping of various gas, solid state, and fiber laser media; medical and aesthetic applications including hair removal; direct diode materials processing; and computer-to-plate (CtP) printing. Many of these applications require high brightness fiber coupled beam delivery, in turn requiring high brightness optical output at the bar and chip level. Many require multiple bars per system, with aggregate powers on the order of kWs, placing a premium on high power and high power conversion efficiency. This paper presents Coherent's recent advances in the production of high power, high brightness, high efficiency bars and chips at 780-830nm. Results are presented for bars and single emitters of various geometries. Performance data is presented demonstrating peak power conversion efficiencies of 63% in CW mode. Reliability data is presented demonstrating <50k hours lifetime for products including 60W 18% fill factor and 80W 28% fill factor conduction cooled bars, and <1e9 shots lifetime for 500W QCW bars.

  15. Heralded quantum repeater based on the scattering of photons off single emitters using parametric down-conversion source.

    Science.gov (United States)

    Song, Guo-Zhu; Wu, Fang-Zhou; Zhang, Mei; Yang, Guo-Jian

    2016-06-28

    Quantum repeater is the key element in quantum communication and quantum information processing. Here, we investigate the possibility of achieving a heralded quantum repeater based on the scattering of photons off single emitters in one-dimensional waveguides. We design the compact quantum circuits for nonlocal entanglement generation, entanglement swapping, and entanglement purification, and discuss the feasibility of our protocols with current experimental technology. In our scheme, we use a parametric down-conversion source instead of ideal single-photon sources to realize the heralded quantum repeater. Moreover, our protocols can turn faulty events into the detection of photon polarization, and the fidelity can reach 100% in principle. Our scheme is attractive and scalable, since it can be realized with artificial solid-state quantum systems. With developed experimental technique on controlling emitter-waveguide systems, the repeater may be very useful in long-distance quantum communication.

  16. Revealing the Nature of Extreme Coronal-line Emitter SDSS J095209.56+214313.3

    CERN Document Server

    Palaversa, Lovro; Sesar, Branimir; Stuart, J Scott; Wozniak, Przemyslaw; Holl, Berry; Ivezić, Željko

    2015-01-01

    Extreme coronal-line emitter (ECLE) SDSSJ095209.56+214313.3, known by its strong, fading, high ionization lines, has been a long standing candidate for a tidal disruption event, however a supernova origin has not yet been ruled out. Here we add several new pieces of information to the puzzle of the nature of the transient that powered its variable coronal lines: 1) an optical light curve from the Lincoln Near Earth Asteroid Research (LINEAR) survey that serendipitously catches the optical flare, and 2) late-time observations of the host galaxy with the Swift Ultraviolet and Optical Telescope (UVOT) and X-ray telescope (XRT) and the ground-based Mercator telescope. The well-sampled, $\\sim10$-year long, unfiltered LINEAR light curve constrains the onset of the flare to a precision of $\\pm5$ days and enables us to place a lower limit on the peak optical magnitude. Difference imaging allows us to estimate the location of the flare in proximity of the host galaxy core. Comparison of the \\textsl{GALEX} data (early ...

  17. REVEALING THE NATURE OF EXTREME CORONAL-LINE EMITTER SDSS J095209.56+214313.3

    Energy Technology Data Exchange (ETDEWEB)

    Palaversa, Lovro; Holl, Berry [Observatoire astronomique de l’Université de Genève, 51 chemin des Maillettes, CH-1290 Sauverny (Switzerland); Gezari, Suvi [Department of Astronomy, University of Maryland, College Park, MD 20742-2421 (United States); Sesar, Branimir [Max Planck Institute for Astronomy, Königstuhl 17, D-69117 Heidelberg (Germany); Stuart, J. Scott [Lincoln Laboratory, Massachusetts Institute of Technology, 244 Wood Street, Lexington, MA 02420-9108 (United States); Wozniak, Przemyslaw [Los Alamos National Laboratory, 30 Bikini Atoll Road, Los Alamos, NM 87545-0001 (United States); Ivezić, Željko, E-mail: lovro.palaversa@unige.ch [University of Washington, Department of Astronomy, P.O. Box 351580, Seattle, WA 98195-1580 (United States)

    2016-03-10

    Extreme coronal-line emitter (ECLE) SDSS J095209.56+214313.3, known by its strong, fading, high-ionization lines, has been a long-standing candidate for a tidal disruption event; however, a supernova (SN) origin has not yet been ruled out. Here we add several new pieces of information to the puzzle of the nature of the transient that powered its variable coronal lines: (1) an optical light curve from the Lincoln Near Earth Asteroid Research (LINEAR) survey that serendipitously catches the optical flare, and (2) late-time observations of the host galaxy with the Swift Ultraviolet and Optical Telescope (UVOT) and X-ray telescope (XRT) and the ground-based Mercator telescope. The well-sampled, ∼10 yr long, unfiltered LINEAR light curve constrains the onset of the flare to a precision of ±5 days and enables us to place a lower limit on the peak optical magnitude. Difference imaging allows us to estimate the location of the flare in proximity of the host galaxy core. Comparison of the GALEX data (early 2006) with the recently acquired Swift UVOT (2015 June) and Mercator observations (2015 April) demonstrates a decrease in the UV flux over a ∼10 yr period, confirming that the flare was UV-bright. The long-lived UV-bright emission, detected 1.8 rest-frame years after the start of the flare, strongly disfavors an SN origin. These new data allow us to conclude that the flare was indeed powered by the tidal disruption of a star by a supermassive black hole and that tidal disruption events are in fact capable of powering the enigmatic class of ECLEs.

  18. Vertically integrated (Ga, In)N nanostructures for future single photon emitters operating in the telecommunication wavelength range.

    Science.gov (United States)

    Winden, A; Mikulics, M; Grützmacher, D; Hardtdegen, H

    2013-10-11

    Important technological steps are discussed and realized for future room-temperature operation of III-nitride single photon emitters. First, the growth technology of positioned single pyramidal InN nanostructures capped by Mg-doped GaN is presented. The optimization of their optical characteristics towards narrowband emission in the telecommunication wavelength range is demonstrated. In addition, a device concept and technology was developed so that the nanostructures became singularly addressable. It was found that the nanopyramids emit in the telecommunication wavelength range if their size is chosen appropriately. A p-GaN contacting layer was successfully produced as a cap to the InN pyramids and the top p-contact was achievable using an intrinsically conductive polymer PEDOT:PSS, allowing a 25% increase in light transmittance compared to standard Ni/Au contact technology. Single nanopyramids were successfully integrated into a high-frequency device layout. These decisive technology steps provide a promising route to electrically driven and room-temperature operating InN based single photon emitters in the telecommunication wavelength range.

  19. Faint Submillimeter Galaxies Revealed by Multifield Deep ALMA Observations: Number Counts, Spatial Clustering, and Dark Submillimeter Emitters

    CERN Document Server

    Ono, Yoshiaki; Kurono, Yasutaka; Momose, Rieko

    2014-01-01

    We present the statistics of faint submillimeter/millimeter galaxies (SMGs) and serendipitous detections of submillimeter/millimeter emitters (SMEs) with no multi-wavelength continuum counterpart revealed by the deep ALMA observations. We identify faint SMGs with flux densities of 0.1-1.0 mJy in the deep Band 6 and Band 7 maps of 10 independent fields that reduce cosmic variance effects. The differential number counts at 1.2 mm are found to increase with decreasing flux density down to 0.1 mJy. Our number counts indicate that the faint (0.1-1.0 mJy, or SFR_IR ~ 30-300 Msun/yr) SMGs contribute nearly a half of the extragalactic background light (EBL), while the remaining half of the EBL is mostly contributed by very faint sources with flux densities of 1 mJy) SMGs, but comparable with abundant high-z star-forming populations such as sBzKs, LBGs, and LAEs. Finally, we report the serendipitous detections of SMEs with continuum counterparts neither in our 1.2 mm-band nor multi-wavelength images including ultra de...

  20. Heralded quantum repeater based on the scattering of photons off single emitters in one-dimensional waveguides

    Energy Technology Data Exchange (ETDEWEB)

    Song, Guo-Zhu; Zhang, Mei; Ai, Qing; Yang, Guo-Jian [Department of Physics, Applied Optics Beijing Area Major Laboratory, Beijing Normal University, Beijing 100875 (China); Alsaedi, Ahmed; Hobiny, Aatef [NAAM-Research Group, Department of Mathematics, Faculty of Science, King Abdulaziz University, P.O. Box 80203, Jeddah 21589 (Saudi Arabia); Deng, Fu-Guo, E-mail: fgdeng@bnu.edu.cn [Department of Physics, Applied Optics Beijing Area Major Laboratory, Beijing Normal University, Beijing 100875 (China); NAAM-Research Group, Department of Mathematics, Faculty of Science, King Abdulaziz University, P.O. Box 80203, Jeddah 21589 (Saudi Arabia)

    2017-03-15

    We propose a heralded quantum repeater based on the scattering of photons off single emitters in one-dimensional waveguides. We show the details by implementing nonlocal entanglement generation, entanglement swapping, and entanglement purification modules with atoms in waveguides, and discuss the feasibility of the repeater with currently achievable technology. In our scheme, the faulty events can be discarded by detecting the polarization of the photons. That is, our protocols are accomplished with a fidelity of 100% in principle, which is advantageous for implementing realistic long-distance quantum communication. Moreover, additional atomic qubits are not required, but only a single-photon medium. Our scheme is scalable and attractive since it can be realized in solid-state quantum systems. With the great progress on controlling atom-waveguide systems, the repeater may be very useful in quantum information processing in the future.

  1. Ghostly Glow Reveals a Hidden Class of Long-Wavelength Radio Emitters

    Science.gov (United States)

    2008-10-01

    (Washington, DC. 08)- A team of scientists, including astronomers from the Naval Research Laboratory (NRL), have detected long wavelength radio emission from a colliding, massive galaxy cluster which, surprisingly, is not detected at the shorter wavelengths typically seen in these objects. The discovery implies that existing radio telescopes have missed a large population of these colliding objects. It also provides an important confirmation of the theoretical prediction that colliding galaxy clusters accelerate electrons and other particles to very high energies through the process of turbulent waves. The team revealed their findings in the October 16, 2008 edition of Nature. This new population of objects is most easily detected at long wavelengths. Professor Greg Taylor of the University of New Mexico and scientific director of the Long Wavelength Array (LWA) points out, "This result is just the tip of the iceberg. When an emerging suite of much more powerful low frequency telescopes, including the LWA in New Mexico, turn their views to the cosmos, the sky will 'light up' with hundreds or even thousands of colliding galaxy clusters." NRL has played a key role in promoting the development of this generation of new instruments and is currently involved with the development of the LWA. NRL radio astronomer and LWA Project Scientist Namir Kassim says "Our discovery of a previously hidden class of low frequency cluster-radio sources is particularly important since the study of galaxy clusters was a primary motivation for development of the LWA." The discovery of the emission in the galaxy cluster Abell 521 (or A521 for short) was made using the Giant Metrewave Radiotelescope (GMRT) in India, and its long wavelength nature was confirmed by the National Science Foundation's (NRAO) Very Large Array (VLA) radio telescope in New Mexico. The attached image shows the radio emission at a wavelength of 125cm in red superimposed on a blue image made from data taken by the

  2. Effect of increased crystallinity of single-walled carbon nanotubes used as field emitters on their electrical properties

    Energy Technology Data Exchange (ETDEWEB)

    Shimoi, Norihiro, E-mail: shimoi@mail.kankyo.tohoku.ac.jp [Graduate School of Environmental Studies, Tohoku University, 6-6-20 Aoba, Aramaki, Aoba-ku, Sendai 980-8579 (Japan)

    2015-12-07

    Single-walled carbon nanotubes (SWCNTs) synthesized by arc discharge are expected to exhibit good field emission (FE) properties at a low driving voltage. We used a coating containing homogeneously dispersed highly crystalline SWCNTs produced by a high-temperature annealing process to fabricate an FE device by a wet-coating process at a low cost. Using the coating, we succeeded in reducing the power consumption of field emitters for planar lighting devices. SWCNTs synthesized by arc discharge have crystal defects in the carbon network, which are considered to induce inelastic electron tunneling that deteriorates the electrical conductivity of the SWCNTs. In this study, the blocking of the transport of electrons in SWCNTs with crystal defects is simulated using an inelastic electron tunneling model. We succeeded in clarifying the mechanism underlying the electrical conductivity of SWCNTs by controlling their crystallinity. In addition, it was confirmed that field emitters using highly crystalline SWCNTs can lead to new applications operating with low power consumption and new devices that may change our daily lives in the future.

  3. Generation of two-lobe light fields with a rotating intensity distribution under propagation for single emitter spectroscopy

    Science.gov (United States)

    Volostnikov, V. G.; Vorontsov, E. N.; Kotova, S. P.; Losevsky, N. N.; Prokopova, D. V.; Razueva, E. V.; Samagin, S. A.

    2016-12-01

    The paper outlines the results of studies on the generation of two-lobe light fields with the intensity distribution rotating during the field propagation. Such fields are needed to determine the depth of bedding of single emitters in spectral studies of substance properties. On the base of the spiral beam optics, the phase distributions were obtained for the synthesis of two-lobe fields with different speeds of rotation of the intensity distribution. The light fields have been formed by using a liquid-crystal spatial phase modulator HOLOEYE HEO-1080P. The influence of the illuminating beam parameters and the aberrations of the system on the quality of the formed light field was also studied.

  4. Heterostructures with CdTe/ZnTe quantum dots for single photon emitters grown by molecular beam epitaxy

    Science.gov (United States)

    Sorokin, S. V.; Sedova, I. V.; Gronin, S. V.; Belyaev, K. G.; Rakhlin, M. V.; Toropov, A. A.; Mukhin, I. S.; Ivanov, S. V.

    2016-12-01

    We report on the molecular beam epitaxy (MBE) of heterostructures with CdTe/ZnTe quantum dots (QDs) with relatively low surface density, which could be used as single-photon emitters. The QDs were formed on the surface of a 3.1- to 4.5-monolayer-thick two-dimensional strained CdTe layer by depositing amorphous Te layer and its fast thermal desorption. Subsequent thermal annealing of the surface with QDs in the absence of external Te flux led to strong broadening and short-wavelength shift of the QD photoluminescence (PL) peak. Measurement of the micro-PL spectra of individual CdTe/ZnTe quantum dots in fabricated mesastructures with a diameter of 200—1000 nm allowed estimation of the QD surface density as 1010 cm-2.

  5. Generation of two-lobe light fields with a rotating intensity distribution under propagation for single emitter spectroscopy

    Directory of Open Access Journals (Sweden)

    Volostnikov V.G.

    2017-01-01

    Full Text Available The paper outlines the results of studies on the generation of two-lobe light fields with the intensity distribution rotating during the field propagation. Such fields are needed to determine the depth of bedding of single emitters in spectral studies of substance properties. On the base of the spiral beam optics, the phase distributions were obtained for the synthesis of two-lobe fields with different speeds of rotation of the intensity distribution. The light fields have been formed by using a liquid-crystal spatial phase modulator HOLOEYE HEO-1080P. The influence of the illuminating beam parameters and the aberrations of the system on the quality of the formed light field was also studied.

  6. A Single Pulse Beam Emittance Measurement for the CERN Heavy Ion Linac

    CERN Document Server

    Crescenti, M

    1995-01-01

    A new device for transverse emittance measurement has been installed in the 4.2 MeV/u filter region of the CERN Heavy Ion Linac (Linac 3). It allows to obtain pulse-to-pulse (every 1.2 sec) visualisation of the Linac 3 beam parameters in order to tune the machine and to match the beam for injection into the first circular accelerator, the PS Booster. The system is based on the "multi-slit" technique similar to the well-known "pepper pot" method. A plate with a series of horizontal or vertical slits is placed in the beam, defining positions in the phase plane. Particles pass through the slits and drift to a scintillator screen where they produce light. The screen is looked at by an externally triggered high resolution CCD camera. For each slit position the light intensity distribution, in the limit of infinitesimal slit aperture, is proportional to the angle distribution of the particles and therefore, provides the angular distribution in the phase plane. The video signal from the camera is digitised and the r...

  7. Faint submillimeter galaxies revealed by multifield deep ALMA observations: number counts, spatial clustering, and a dark submillimeter line emitter

    Energy Technology Data Exchange (ETDEWEB)

    Ono, Yoshiaki; Ouchi, Masami; Momose, Rieko [Institute for Cosmic Ray Research, The University of Tokyo, Kashiwa, Chiba 277-8582 (Japan); Kurono, Yasutaka, E-mail: ono@icrr.u-tokyo.ac.jp [Joint ALMA Observatory, Alonso de Cordova 3107, Vitacura, Santiago 763-0355 (Chile)

    2014-11-01

    We present the statistics of faint submillimeter/millimeter galaxies (SMGs) and serendipitous detections of a submillimeter/millimeter line emitter (SLE) with no multi-wavelength continuum counterpart revealed by the deep ALMA observations. We identify faint SMGs with flux densities of 0.1-1.0 mJy in the deep Band-6 and Band-7 maps of 10 independent fields that reduce cosmic variance effects. The differential number counts at 1.2 mm are found to increase with decreasing flux density down to 0.1 mJy. Our number counts indicate that the faint (0.1-1.0 mJy, or SFR{sub IR} ∼ 30-300 M {sub ☉} yr{sup –1}) SMGs contribute nearly a half of the extragalactic background light (EBL), while the remaining half of the EBL is mostly contributed by very faint sources with flux densities of <0.1 mJy (SFR{sub IR} ≲ 30 M {sub ☉} yr{sup –1}). We conduct counts-in-cells analysis with multifield ALMA data for the faint SMGs, and obtain a coarse estimate of galaxy bias, b {sub g} < 4. The galaxy bias suggests that the dark halo masses of the faint SMGs are ≲ 7 × 10{sup 12} M {sub ☉}, which is smaller than those of bright (>1 mJy) SMGs, but consistent with abundant high-z star-forming populations, such as sBzKs, LBGs, and LAEs. Finally, we report the serendipitous detection of SLE-1, which has no continuum counterparts in our 1.2 mm-band or multi-wavelength images, including ultra deep HST/WFC3 and Spitzer data. The SLE has a significant line at 249.9 GHz with a signal-to-noise ratio of 7.1. If the SLE is not a spurious source made by the unknown systematic noise of ALMA, the strong upper limits of our multi-wavelength data suggest that the SLE would be a faint galaxy at z ≳ 6.

  8. Emitter spacing effects on field emission properties of laser-treated single-walled carbon nanotube buckypapers.

    Science.gov (United States)

    Chen, YiWen; Miao, Hsin-Yuan; Lin, Ryan Jiyao; Zhang, Mei; Liang, Richard; Zhang, Chuck; Wang, Ben

    2010-12-10

    Carbon nanotube (CNT) emitters on buckypaper were activated by laser treatment and their field emission properties were investigated. The pristine buckypapers and CNT emitters' height, diameter, and spacing were characterized through optical analysis. The emitter spacing directly impacted the emission results when the laser power and treatment times were fixed. The increasing emitter density increased the enhanced field emission current and luminance. However, a continuous and excessive increase of emitter density with spacing reduction generated the screening effect. As a result, the extended screening effect from the smaller spacing eventually crippled the field emission effectiveness. Luminance intensity and uniformity of field emission suggest that the highly effective buckypaper will have a density of 2500 emission spots cm(-2), which presents an effective field enhancement factor of 3721 and a moderated screening effect of 0.005. Proper laser treatment is an effective post-treatment process for optimizing field emission, luminance, and durability performance for buckypaper cold cathodes.

  9. Azimuth calculation for buried pipelines using a synthetic array of emitters, a single survey line and scattering matrix formalism

    Science.gov (United States)

    Bullo, Darío; Villela, Almendra; Bonomo, Néstor

    2016-11-01

    We evaluate the simultaneous application of a synthetic-emitter array (SEA) methodology and formulation derived from the analysis of the rotation transformations of the scattering matrix (RTSM) to calculate the orientation of buried pipes from GPR data acquired along a single survey line. The main objective of this study is to analyze if the SEA-RTSM combination can improve the azimuth calculation obtained from the usual single-offset-RTSM (SO-RTSM) procedure. This possibility is based on the SEA ability of increasing the continuity and amplitude of the primary reflections with respect to the background clutter and noise, which is expected to reduce the fluctuations involved in the RTSM calculation of the azimuth, so that its accuracy and precision are improved. A SEA methodology designed to be used in conjunction with the RTSM methodology is described. A procedure that optimizes the results of the SEA methodology is explained. A statistical RTSM calculation is adopted in order to obtain the final azimuth. Different relevant parameters of the soil and the array of emitters are varied in order to evaluate the SEA-RTSM methodology and its results. Numerically simulated and experimental data are used in this evaluation. The SEA-RTSM and the SO-RTSM results are compared between them. These results are also compared with an equivalent common-midpoint-RTSM (CMP-RTSM) calculation. Improved precision and accuracy are obtained from the SEA-RTSM methodology in the great majority of the examples. The height/width of the resulting azimuth distribution increases 102% in average when using this procedure instead of the usual SO-RTSM procedure, the average standard deviation diminishes 12%, and the average differences between the calculated and true azimuths reduce 34%. Minor improvements with respect to SO are obtained with the CMP-RTSM methodology. The proposed SEA-RTSM methodology and its results are especially relevant in civil engineering applications in which it is

  10. Emittance Reduction between EBIS LINAC and Booster by Electron Beam Cooling; Is Single Pass Cooling Possible?

    Energy Technology Data Exchange (ETDEWEB)

    Hershcovitch,A.

    2008-04-01

    Electron beam cooling is examined as an option to reduce momentum of gold ions exiting the EBIS LINAC before injection into the booster. Electron beam parameters are based on experimental data (obtained at BNL) of electron beams extracted from a plasma cathode. Preliminary calculations indicate that single pass cooling is feasible; momentum spread can be reduced by more than an order of magnitude in less than one meter.

  11. Proton transfer and photoluminescence intermittency of single emitters in dyed crystals.

    Science.gov (United States)

    Riley, Erin A; Hess, Chelsea M; Pioquinto, Jan Rey L; Kaminsky, Werner; Kahr, Bart; Reid, Philip J

    2013-04-25

    The role of proton transfer in the photoluminescence intermittency (PI) of single molecules of violamine R (VR) overgrown in potassium acid phthalate (KAP) crystals is evaluated in comparisons of protonated (KAP) and deuterated (DKAP) mixed crystals between 23 and 60 °C. The PI is analyzed by the construction of cumulative distribution functions that are statistically compared. We find that the on- and off-interval duration distributions change with isotopic substitution consistent with proton transfer contributing to the PI of VR. The on- and off-interval duration distributions have distinct temperature dependencies consistent with different mechanisms for dark state production and decay. Additional evidence for proton-transfer is provided by distributions of single molecule emission-energy maxima that reflect emission from protonated and deprotonated VR. A mechanism for the PI of KAP is presented, where the dark state is assigned to formation of the colorless, leuco form of VR, formed by proton transfer from VR to the KAP lattice, and decay of the dark state involves ring-opening promoted by proton transfer from KAP to VR. The distributed kinetics for dark-state production and decay are modeled using a log-normal distribution for the PI data in preference to a power-law previously assumed. A discussion of the log-normal distribution with regards to PI and proton transfer is presented.

  12. Real-time simulation of finite-frequency noise from a single-electron emitter

    Science.gov (United States)

    Jonckheere, T.; Stoll, T.; Rech, J.; Martin, T.

    2012-01-01

    We study the real-time emission of single electrons from a quantum dot coupled to a one dimensional conductor, using exact diagonalization on a discrete tight-binding chain. We show that, from the calculation of the time evolution of the one-electron states, we have simple access to all the relevant physical quantities in the system. In particular, we are able to compute accurately the finite-frequency current autocorrelation noise. The method that we use is general and versatile, allowing us to study the impact of many different parameters, such as the dot transparency or level position. Our results can be directly compared with existing experiments, and can also serve as a basis for future calculations including electronic interactions using the time-dependent density-matrix renormalization group and other techniques based on tight-binding models.

  13. Control of single photon emitters in semiconductor nanowires by surface acoustic waves

    Science.gov (United States)

    Lazić, S.; Hernández-Mínguez, A.; Santos, P. V.

    2017-08-01

    We report on an experimental study into the effects of surface acoustic waves on the optical emission of dot-in-a-nanowire heterostructures in III-V material systems. Under direct optical excitation, the excitonic energy levels in III-nitride dot-in-a-nanowire heterostructures oscillate at the acoustic frequency, producing a characteristic splitting of the emission lines in the time-integrated photoluminescence spectra. This acoustically induced periodic tuning of the excitonic transition energies is combined with spectral detection filtering and employed as a tool to regulate the temporal output of anti-bunched photons emitted from these nanowire quantum dots. In addition, the acoustic transport of electrons and holes along a III-arsenide nanowire injects the electric charges into an ensemble of quantum dot-like recombination centers that are spatially separated from the optical excitation area. The acoustic population and depopulation mechanism determines the number of carrier recombination events taking place simultaneously in the ensemble, thus allowing control of the anti-bunching degree of the emitted photons. The results presented are relevant for the dynamic control of single photon emission in III-V semiconductor heterostructures.

  14. TinyLev: A multi-emitter single-axis acoustic levitator

    Science.gov (United States)

    Marzo, Asier; Barnes, Adrian; Drinkwater, Bruce W.

    2017-08-01

    Acoustic levitation has the potential to enable novel studies due to its ability to hold a wide variety of substances against gravity under container-less conditions. It has found application in spectroscopy, chemistry, and the study of organisms in microgravity. Current levitators are constructed using Langevin horns that need to be manufactured to high tolerance with carefully matched resonant frequencies. This resonance condition is hard to maintain as their temperature changes due to transduction heating. In addition, Langevin horns are required to operate at high voltages (>100 V) which may cause problems in challenging experimental environments. Here, we design, build, and evaluate a single-axis levitator based on multiple, low-voltage (ca. 20 V), well-matched, and commercially available ultrasonic transducers. The levitator operates at 40 kHz in air and can trap objects above 2.2 g/cm3 density and 4 mm in diameter whilst consuming 10 W of input power. Levitation of water, fused-silica spheres, small insects, and electronic components is demonstrated. The device is constructed from low-cost off-the-shelf components and is easily assembled using 3D printed sections. Complete instructions and a part list are provided on how to assemble the levitator.

  15. Single-Crystalline Silicon Solar Cell with Selective Emitter Formed by Screen Printing and Chemical Etching Method: A Feasibility Study

    Directory of Open Access Journals (Sweden)

    Yen-Po Chen

    2013-01-01

    Full Text Available A new method for fabricating crystalline silicon solar cells with selective emitters is presented. In this method, shallow trenches corresponding to metal contact area are first formed by screen printing and chemical etching, followed by heavy doping over the whole front surface of the silicon wafer. After a polymer mask is pasted by aligned screen-printing to cover the shallow trenches, the silicon wafer is etched such that the heavy doping remains at the shallow trench area, while other areas become lightly doped. With the presented method, two screening printing steps are required for obtaining a selective emitter structure on a solar wafer. Compared with existing etch-back methods, the presented one is believed to be able to easily conform with present industrial process. Experimental results show that optical responses at the short and long wavelengths were both improved by applying the proposed selective emitter technique to fabricate solar cells with an a-Si:H film deposited on the back surface. The selective emitter cell with a-Si:H back surface deposition had improvements of 1.66 mA/cm2 and 1.23% absolute in Jsc and conversion efficiency, respectively, compared to the reference cell that had a homogeneous emitter and no a-Si:H on the back surface.

  16. Calculation of the detection efficiency in liquid scintillators. I.- Single negatrons emitters; Calculo de la eficiencia de deteccion en liquidos centelleadores. I. Nucleidos que se desintegran por emision simple de negatrones

    Energy Technology Data Exchange (ETDEWEB)

    Grau Malonda, A.; Garcia-torano, E.

    1981-07-01

    Counting efficiency for 62 single beta emitters has been computed from the beta energy distribution, the figure of merit and the ionization quenching. Efficiency v.s. figure of merit is plotted and tabulated. (Author) 16 refs.

  17. Herschel reveals the obscured star formation in HiZELS H\\alpha\\ emitters at z=1.47

    CERN Document Server

    Ibar, E; Best, P N; Ivison, R J; Smail, I; Arumugam, V; Berta, S; Béthermin, M; Bock, J; Cava, A; Conley, A; Farrah, D; Floc'h, E Le; Lutz, D; Magdis, G; Magnelli, B; Ikarashi, S; Kohno, K; Marsden, G; Oliver, S J; Page, M J; Pozzi, F; Riguccini, L; Schulz, B; Seymour, N; Smith, A J; Symeonidis, M; Wang, L; Wardlow, J; Zemcov, M

    2013-01-01

    We describe the far-infrared (FIR; rest-frame 8--1000\\mu m) properties of a sample of 443 H\\alpha-selected star-forming galaxies in the COSMOS and UDS fields detected by the HiZELS imaging survey. Sources are identified using narrow-band filters in combination with broad-band photometry to uniformly select H\\alpha\\ (and [OII] if available) emitters in a narrow redshift slice at z = 1.47+/-0.02. We use a stacking approach in Spitzer, Herschel (from PEP and HerMES surveys) and AzTEC images to describe their typical FIR properties. We find that HiZELS galaxies with observed H\\alpha\\ luminosities of ~ 10^{8.1-9.1} Lo have bolometric FIR luminosities of typical LIRGs, L_FIR ~ 10^{11.48+/-0.05} Lo. Combining the H\\alpha\\ and FIR luminosities, we derive median SFR = 32+/-5 Mo/yr and H\\alpha\\ extinctions of A(H\\alpha) = 1.0+/-0.2 mag. Perhaps surprisingly, little difference is seen in typical HiZELS extinction levels compared to local star-forming galaxies. We confirm previous empirical stellar mass (M*) to A(H\\alpha...

  18. Triggered mesa-top single photon emitter arrays and on-chip integration with dielectric nanoantenna-waveguide systems

    CERN Document Server

    Zhang, Jiefei; Lu, Siyuan; Madhukar, Anupam

    2016-01-01

    Nanophotonic quantum information processing systems require spatially ordered, spectrally uniform single photon sources (SPSs), integrated on-chip with co-designed light manipulating elements providing emission rate enhancement, emitted photon guidance, and lossless propagation. Towards this objective, we introduce and report on systems comprising an SPS array with each SPS surrounded by a dielectric building block (DBB) based multifunctional light manipulation unit (LMU). For the SPS array, we report triggered single photon emission at 77K from GaAs(001)/InGaAs single quantum dots (SQDs) grown selectively on top of nanomesas using the approach of substrate-encoded size-reducing epitaxy (SESRE). Systematic temperature and power dependent photoluminescence (PL), PL excitation, time-resolved PL, and emission statistics studies reveal high spectral uniformity and single photon emission at 77.4K with $g^{(2)}$(0) of 0.24 $\\pm$ 0.07. The SESRE based SPS arrays, following growth of a planarizing overlayer, are read...

  19. Herschel reveals the obscured star formation in HiZELS Hα emitters at z = 1.47

    Science.gov (United States)

    Ibar, E.; Sobral, D.; Best, P. N.; Ivison, R. J.; Smail, I.; Arumugam, V.; Berta, S.; Béthermin, M.; Bock, J.; Cava, A.; Conley, A.; Farrah, D.; Geach, J.; Ikarashi, S.; Kohno, K.; Le Floc'h, E.; Lutz, D.; Magdis, G.; Magnelli, B.; Marsden, G.; Oliver, S. J.; Page, M. J.; Pozzi, F.; Riguccini, L.; Schulz, B.; Seymour, N.; Smith, A. J.; Symeonidis, M.; Wang, L.; Wardlow, J.; Zemcov, M.

    2013-10-01

    We describe the far-infrared (far-IR; rest-frame 8-1000-μm) properties of a sample of 443 Hα-selected star-forming galaxies in the Cosmic Evolution Survey (COSMOS) and Ultra Deep Survey (UDS) fields detected by the High-redshift Emission Line Survey (HiZELS) imaging survey. Sources are identified using narrow-band filters in combination with broad-band photometry to uniformly select Hα (and [O II] if available) emitters in a narrow redshift slice at z = 1.47 ± 0.02. We use a stacking approach in Spitzer-MIPS mid-IR, Herschel-PACS/SPIRE far-IR [from the PACS Evolutionary Prove (PEP) and Herschel Multi-tiered Extragalactic Survey (HerMES)] and AzTEC mm-wave images to describe their typical far-IR properties. We find that HiZELS galaxies with observed Hα luminosities of L(Hα)obs ≈ 108.1-9.1 L⊙ ( ≈ 1041.7-42.7 erg s-1) have bolometric far-IR luminosities of typical luminous IR galaxies, L(8-1000 μ m)≈ 10^{11.41^{+0.04}_{-0.06}} L⊙. Combining the Hα and far-IR luminosities, we derive median star formation rates (SFRs) of SFRHα, FIR = 32 ± 5 M⊙ yr-1 and Hα extinctions of AHα = 1.0 ± 0.2 mag. Perhaps surprisingly, little difference is seen in typical HiZELS extinction levels compared to local star-forming galaxies. We confirm previous empirical stellar mass (M*) to AHα relations and the little or no evolution up to z = 1.47. For HiZELS galaxies (or similar samples) we provide an empirical parametrization of the SFR as a function of rest-frame (u - z) colours and 3.6-μm photometry - a useful proxy to aid in the absence of far-IR detections in high-z galaxies. We find that the observed Hα luminosity is a dominant SFR tracer when rest-frame (u - z) colours are ≲0.9 mag or when Spitzer-3.6-μm photometry is fainter than 22 mag (Vega) or when stellar masses are lower than 109.7 M⊙. We do not find any correlation between the [O II]/Hα and far-IR luminosity, suggesting that this emission line ratio does not trace the extinction of the most

  20. Hybrid emitter all back contact solar cell

    Science.gov (United States)

    Loscutoff, Paul; Rim, Seung

    2016-04-12

    An all back contact solar cell has a hybrid emitter design. The solar cell has a thin dielectric layer formed on a backside surface of a single crystalline silicon substrate. One emitter of the solar cell is made of doped polycrystalline silicon that is formed on the thin dielectric layer. The other emitter of the solar cell is formed in the single crystalline silicon substrate and is made of doped single crystalline silicon. The solar cell includes contact holes that allow metal contacts to connect to corresponding emitters.

  1. Brownian Emitters

    Science.gov (United States)

    Tsekov, Roumen

    2016-06-01

    A Brownian harmonic oscillator, which dissipates energy either by friction or via emission of electromagnetic radiation, is considered. This Brownian emitter is driven by the surrounding thermo-quantum fluctuations, which are theoretically described by the fluctuation-dissipation theorem. It is shown how the Abraham-Lorentz force leads to dependence of the half-width on the peak frequency of the oscillator amplitude spectral density. It is found that for the case of a charged particle moving in vacuum at zero temperature, its root-mean-square velocity fluctuation is a universal constant, equal to roughly 1/18 of the speed of light. The relevant Fokker-Planck and Smoluchowski equations are also derived.

  2. Asymmetrical field emitter

    Science.gov (United States)

    Fleming, J.G.; Smith, B.K.

    1995-10-10

    A method is disclosed for providing a field emitter with an asymmetrical emitter structure having a very sharp tip in close proximity to its gate. One preferred embodiment of the present invention includes an asymmetrical emitter and a gate. The emitter having a tip and a side is coupled to a substrate. The gate is connected to a step in the substrate. The step has a top surface and a side wall that is substantially parallel to the side of the emitter. The tip of the emitter is in close proximity to the gate. The emitter is at an emitter potential, and the gate is at a gate potential such that with the two potentials at appropriate values, electrons are emitted from the emitter. In one embodiment, the gate is separated from the emitter by an oxide layer, and the emitter is etched anisotropically to form its tip and its asymmetrical structure. 17 figs.

  3. Mitochondrial specialization revealed by single muscle fiber proteomics

    DEFF Research Database (Denmark)

    Schiaffino, S; Reggiani, C; Kostrominova, T Y

    2015-01-01

    We have developed a highly sensitive mass spectrometry-based proteomic workflow to examine the proteome of single muscle fibers. This study revealed significant differences in the mitochondrial proteome of the four major fiber types present in mouse skeletal muscle. Here, we focus on Krebs cycle ...... scavenging capacity to cope with the higher levels of reactive oxygen species production....

  4. Quantitative single-particle digital autoradiography with α-particle emitters for targeted radionuclide therapy using the iQID camera

    Energy Technology Data Exchange (ETDEWEB)

    Miller, Brian W., E-mail: brian.miller@pnnl.gov [Pacific Northwest National Laboratory, Richland, Washington 99354 and College of Optical Sciences, The University of Arizona, Tucson, Arizona 85719 (United States); Frost, Sofia H. L.; Frayo, Shani L.; Kenoyer, Aimee L.; Santos, Erlinda; Jones, Jon C.; Orozco, Johnnie J. [Fred Hutchinson Cancer Research Center, Seattle, Washington 98109 (United States); Green, Damian J.; Press, Oliver W.; Pagel, John M.; Sandmaier, Brenda M. [Fred Hutchinson Cancer Research Center, Seattle, Washington 98109 and Department of Medicine, University of Washington, Seattle, Washington 98195 (United States); Hamlin, Donald K.; Wilbur, D. Scott [Department of Radiation Oncology, University of Washington, Seattle, Washington 98195 (United States); Fisher, Darrell R. [Dade Moeller Health Group, Richland, Washington 99354 (United States)

    2015-07-15

    Purpose: Alpha-emitting radionuclides exhibit a potential advantage for cancer treatments because they release large amounts of ionizing energy over a few cell diameters (50–80 μm), causing localized, irreparable double-strand DNA breaks that lead to cell death. Radioimmunotherapy (RIT) approaches using monoclonal antibodies labeled with α emitters may thus inactivate targeted cells with minimal radiation damage to surrounding tissues. Tools are needed to visualize and quantify the radioactivity distribution and absorbed doses to targeted and nontargeted cells for accurate dosimetry of all treatment regimens utilizing α particles, including RIT and others (e.g., Ra-223), especially for organs and tumors with heterogeneous radionuclide distributions. The aim of this study was to evaluate and characterize a novel single-particle digital autoradiography imager, the ionizing-radiation quantum imaging detector (iQID) camera, for use in α-RIT experiments. Methods: The iQID camera is a scintillator-based radiation detection system that images and identifies charged-particle and gamma-ray/x-ray emissions spatially and temporally on an event-by-event basis. It employs CCD-CMOS cameras and high-performance computing hardware for real-time imaging and activity quantification of tissue sections, approaching cellular resolutions. In this work, the authors evaluated its characteristics for α-particle imaging, including measurements of intrinsic detector spatial resolutions and background count rates at various detector configurations and quantification of activity distributions. The technique was assessed for quantitative imaging of astatine-211 ({sup 211}At) activity distributions in cryosections of murine and canine tissue samples. Results: The highest spatial resolution was measured at ∼20 μm full width at half maximum and the α-particle background was measured at a rate as low as (2.6 ± 0.5) × 10{sup −4} cpm/cm{sup 2} (40 mm diameter detector area

  5. Quantitative Single-Particle Digital Autoradiography with α-Particle Emitters for Targeted Radionuclide Therapy using the iQID Camera

    Energy Technology Data Exchange (ETDEWEB)

    Miller, Brian W.; Frost, Sophia; Frayo, Shani; Kenoyer, Aimee L.; Santos, E. B.; Jones, Jon C.; Green, Damian J.; Hamlin, Donald K.; Wilbur, D. Scott; Fisher, Darrell R.; Orozco, Johnnie J.; Press, Oliver W.; Pagel, John M.; Sandmaier, B. M.

    2015-07-01

    Abstract Alpha emitting radionuclides exhibit a potential advantage for cancer treatments because they release large amounts of ionizing energy over a few cell diameters (50–80 μm) causing localized, irreparable double-strand DNA breaks that lead to cell death. Radioimmunotherapy (RIT) approaches using monoclonal antibodies labeled with alpha emitters may inactivate targeted cells with minimal radiation damage to surrounding tissues. For accurate dosimetry in alpha-RIT, tools are needed to visualize and quantify the radioactivity distribution and absorbed dose to targeted and non-targeted cells, especially for organs and tumors with heterogeneous radionuclide distributions. The aim of this study was to evaluate and characterize a novel single-particle digital autoradiography imager, iQID (ionizing-radiation Quantum Imaging Detector), for use in alpha-RIT experiments. Methods: The iQID camera is a scintillator-based radiation detection technology that images and identifies charged-particle and gamma-ray/X-ray emissions spatially and temporally on an event-by-event basis. It employs recent advances in CCD/CMOS cameras and computing hardware for real-time imaging and activity quantification of tissue sections, approaching cellular resolutions. In this work, we evaluated this system’s characteristics for alpha particle imaging including measurements of spatial resolution and background count rates at various detector configurations and quantification of activity distributions. The technique was assessed for quantitative imaging of astatine-211 (211At) activity distributions in cryosections of murine and canine tissue samples. Results: The highest spatial resolution was measured at ~20 μm full width at half maximum (FWHM) and the alpha particle background was measured at a rate of (2.6 ± 0.5) × 10–4 cpm/cm2 (40 mm diameter detector area). Simultaneous imaging of multiple tissue sections was performed using a large-area iQID configuration (ø 11.5 cm

  6. Control of spontaneous emission of a single quantum emitter through a time-modulated photonic-band-gap environment

    Science.gov (United States)

    Calajò, Giuseppe; Rizzuto, Lucia; Passante, Roberto

    2017-08-01

    We consider the spontaneous emission of a two-level quantum emitter, such as an atom or a quantum dot, in a modulated time-dependent environment with a photonic band gap. An example of such an environment is a dynamical photonic crystal or any other environment with a band gap whose properties are modulated in time, in the effective mass approximation. After introducing our model of a dynamical photonic crystal, we show that it allows new possibilities to control and tailor the physical features of the emitted radiation, specifically its frequency spectrum. In the weak-coupling limit and in an adiabatic case, we obtain the emitted spectrum and we show the appearance of two lateral peaks due to the presence of the modulated environment, separated from the central peak by the modulation frequency. We show that the two side peaks are not symmetric in height, and that their height ratio can be exploited to investigate the density of states of the environment. Our results show that a dynamical environment can give further possibilities to modify the spontaneous emission features, such as its spectrum and emission rate, with respect to a static one. Observability of the phenomena we obtain is discussed, as well as relevance for tailoring and engineering radiative processes.

  7. Emittance Theory for Thin Film Selective Emitter

    Science.gov (United States)

    Chubb, Donald L.; Lowe, Roland A.; Good, Brian S.

    1994-01-01

    Thin films of high temperature garnet materials such as yttrium aluminum garnet (YAG) doped with rare earths are currently being investigated as selective emitters. This paper presents a radiative transfer analysis of the thin film emitter. From this analysis the emitter efficiency and power density are calculated. Results based on measured extinction coefficients for erbium-YAG and holmium-YAG are presented. These results indicated that emitter efficiencies of 50 percent and power densities of several watts/sq cm are attainable at moderate temperatures (less than 1750 K).

  8. Waveguide coupled resonance fluorescence from on-chip quantum emitter.

    Science.gov (United States)

    Makhonin, Maxim N; Dixon, James E; Coles, Rikki J; Royall, Ben; Luxmoore, Isaac J; Clarke, Edmund; Hugues, Maxime; Skolnick, Maurice S; Fox, A Mark

    2014-12-10

    Resonantly driven quantum emitters offer a very promising route to obtain highly coherent sources of single photons required for applications in quantum information processing (QIP). Realizing this for on-chip scalable devices would be important for scientific advances and practical applications in the field of integrated quantum optics. Here we report on-chip quantum dot (QD) resonance fluorescence (RF) efficiently coupled into a single-mode waveguide, a key component of a photonic integrated circuit, with a negligible resonant laser background and show that the QD coherence is enhanced by more than a factor of 4 compared to off-resonant excitation. Single-photon behavior is confirmed under resonant excitation, and fast fluctuating charge dynamics are revealed in autocorrelation g((2)) measurements. The potential for triggered operation is verified in pulsed RF. These results pave the way to a novel class of integrated quantum-optical devices for on-chip quantum information processing with embedded resonantly driven quantum emitters.

  9. Emittance exchange results

    Energy Technology Data Exchange (ETDEWEB)

    Fliller, R.P., III; /Brookhaven; Koeth, T.; /Rutgers U., Piscataway

    2009-09-01

    The promise of next-generation light sources depends on the availability of ultra-low emittance electron sources. One method of producing low transverse emittance beams is to generate a low longitudinal emittance beam and exchange it with a large transverse emittance. Experiments are underway at Fermilab's A0 Photoinjector and ANL's Argonne Wakefield Accelerator using the exchange scheme of Kim and Sessler. The experiment at the A0 Photoinjector exchanges a large longitudinal emittance with a small transverse emittance. AWA expects to exchange a large transverse emittance with a small longitudinal emittance. In this paper we discuss recent results at A0 and AWA and future plans for these experiments.

  10. Emittance Exchange Results

    Energy Technology Data Exchange (ETDEWEB)

    Fliller III,R.; Koeth, T.

    2009-05-04

    The promise of next-generation light sources depends on the availability of ultra-low emittance electron sources. One method of producing low transverse emittance beams is to generate a low longitudinal emittance beam and exchange it with a large transverse emittance. Experiments are underway at Fermilab's A0 Photoinjector and ANL's Argonne Wakefield Accelerator using the exchange scheme of Kim and Sessler. The experiment at the A0 Photoinjector exchanges a large longitudinal emittance with a small transverse emittance. AWA expects to exchange a large transverse emittance with a small longitudinal emittance. In this paper we discuss recent results at A0 and AWA and future plans for these experiments.

  11. Aberration Corrected Emittance Exchange

    CERN Document Server

    Nanni, Emilio A

    2015-01-01

    Full exploitation of emittance exchange (EEX) requires aberration-free performance of a complex imaging system including active radio-frequency (RF) elements which can add temporal distortions. We investigate the performance of an EEX line where the exchange occurs between two dimensions with normalized emittances which differ by orders of magnitude. The transverse emittance is exchanged into the longitudinal dimension using a double dog-leg emittance exchange setup with a 5 cell RF deflector cavity. Aberration correction is performed on the four most dominant aberrations. These include temporal aberrations that are corrected with higher order magnetic optical elements located where longitudinal and transverse emittance are coupled. We demonstrate aberration-free performance of emittances differing by 4 orders of magnitude, i.e. an initial transverse emittance of $\\epsilon_x=1$ pm-rad is exchanged with a longitudinal emittance of $\\epsilon_z=10$ nm-rad.

  12. Photoacoustic and dielectric spectroscopic studies of 4-dimethylamino-n-methyl-4-stilbazolium tosylate single crystal: An efficient terahertz emitter

    Science.gov (United States)

    Manivannan, M.; Martin Britto Dhas, S. A.; Jose, M.

    2016-12-01

    Bulk terahertz emitting single crystal of 4-dimethylamino-N-methyl-4-stilbazolium tosylate (DAST) was synthesized by condensation method and grown by slow solvent evaporation technique from methanol. The structure and cell parameters of the grown crystals were derived from single crystal and powder X-ray diffraction analyses and the optical properties of the crystal were analyzed by UV-Vis Spectrophotometer. The presence of functional groups was identified by FTIR and FT-Raman spectroscopic studies. We demonstrated that in DAST crystal, the thermal transport properties such as thermal conductivity, thermal diffusivity and thermal effusivity are better than several well recognized standard materials using photoacoustic spectrophotometer. The dielectric measurement was made as a function of frequency (1 Hz-35 MHz) at different temperatures (30-200 °C). The dielectric constant and dielectric loss were found to be strongly dependent on temperature and frequency of the applied electric field. The semicircle in the cole-cole plot showed the presence of dielectric relaxation in the crystal with its diameter representing the resistance of the crystal. The resistivity and ac conductivity were calculated from the measured dielectric data.

  13. Screen printed boron emitters for solar cells

    Energy Technology Data Exchange (ETDEWEB)

    Recart, F.; Freire, I.; Perez, L.; Lago-Aurrekoetxea, R.; Jimeno, J.C.; Bueno, G. [Instituto de Tecnologia Microelectronica, Teknologia Mikroelektronikoaren Institutua UPV/EHU, Alda.Urquijo s/n, 48013 Bilbao (Spain)

    2007-06-15

    Screen printed (SP) boron emitters are presented as a useful option for the manufacturing of p-type emitters of solar cells. Details are provided on the diffusion process, including deposition, drying and firing steps, the latter performed in an infrared belt furnace. Besides their main dependences on the firing conditions, the sheet resistances and dopant profiles of the resulting emitters reveal the relevance of the drying step and the exhaustion limits of the doping source. A characterization of the recombination concludes that moderate emitter saturation currents (J{sub oe}<0.5 pA/cm{sup 2}) and acceptable bulk lifetimes ({tau}{sub B}>40 {mu}s) can be obtained on Czochralski silicon wafers. Finally, Cz n-type 0.7 {omega} cm solar cells are presented, which once again prove the feasibility of SP boron emitters and point to issues regarding their metallization. (author)

  14. Nanoelectrospray emitter arrays providing interemitter electric field uniformity.

    Science.gov (United States)

    Kelly, Ryan T; Page, Jason S; Marginean, Ioan; Tang, Keqi; Smith, Richard D

    2008-07-15

    Arrays of electrospray ionization (ESI) emitters have been reported previously as a means of enhancing ionization efficiency or signal intensity. A key challenge when working with multiple, closely spaced ESI emitters is overcoming the deleterious effects caused by electrical interference among neighboring emitters. Individual emitters can experience different electric fields depending on their relative position in the array, such that it becomes difficult to operate all of the emitters optimally for a given applied potential. In this work, we have developed multi-nanoESI emitters arranged with a circular pattern, which enable the constituent emitters to experience a uniform electric field. The performance of the circular emitter array was compared to a single emitter and to a previously developed linear emitter array, which verified that improved electric field uniformity was achieved with the circular arrangement. The circular arrays were also interfaced with a mass spectrometer via a matching multicapillary inlet, and the results were compared with those obtained using a single emitter. By minimizing interemitter electric field inhomogeneities, much larger arrays having closer emitter spacing should be feasible.

  15. Narrowband terahertz emitters using metamaterial films.

    Science.gov (United States)

    Alves, Fabio; Kearney, Brian; Grbovic, Dragoslav; Karunasiri, Gamani

    2012-09-10

    In this article we report on metamaterial-based narrowband thermal terahertz (THz) emitters with a bandwidth of about 1 THz. Single band emitters designed to radiate in the 4 to 8 THz range were found to emit as high as 36 W/m(2) when operated at 400 °C. Emission into two well-separated THz bands was also demonstrated by using metamaterial structures featuring more complex unit cells. Imaging of heated emitters using a microbolometer camera fitted with THz optics clearly showed the expected higher emissivity from the metamaterial structure compared to low-emissivity of the surrounding aluminum.

  16. Optical Signatures of Quantum Emitters in Suspended Hexagonal Boron Nitride.

    Science.gov (United States)

    Exarhos, Annemarie L; Hopper, David A; Grote, Richard R; Alkauskas, Audrius; Bassett, Lee C

    2017-03-28

    Hexagonal boron nitride (h-BN) is rapidly emerging as an attractive material for solid-state quantum engineering. Analogously to three-dimensional wide-band-gap semiconductors such as diamond, h-BN hosts isolated defects exhibiting visible fluorescence at room temperature, and the ability to position such quantum emitters within a two-dimensional material promises breakthrough advances in quantum sensing, photonics, and other quantum technologies. Critical to such applications is an understanding of the physics underlying h-BN's quantum emission. We report the creation and characterization of visible single-photon sources in suspended, single-crystal, h-BN films. With substrate interactions eliminated, we study the spectral, temporal, and spatial characteristics of the defects' optical emission. Theoretical analysis of the defects' spectra reveals similarities in vibronic coupling to h-BN phonon modes despite widely varying fluorescence wavelengths, and a statistical analysis of the polarized emission from many emitters throughout the same single-crystal flake uncovers a weak correlation between the optical dipole orientations of some defects and h-BN's primitive crystallographic axes, despite a clear misalignment for other dipoles. These measurements constrain possible defect models and, moreover, suggest that several classes of emitters can exist simultaneously throughout free-standing h-BN, whether they be different defects, different charge states of the same defect, or the result of strong local perturbations.

  17. Spontaneous Fluctuations of Transition Dipole Moment Orientation in OLED Triplet Emitters.

    Science.gov (United States)

    Steiner, Florian; Bange, Sebastian; Vogelsang, Jan; Lupton, John M

    2015-03-19

    The efficiency of an organic light-emitting diode (OLED) depends on the microscopic orientation of transition dipole moments of the molecular emitters. The most effective materials used for light generation have 3-fold symmetry, which prohibits a priori determination of dipole orientation due to the degeneracy of the fundamental transition. Single-molecule spectroscopy reveals that the model triplet emitter tris(1-phenylisoquinoline)iridium(III) (Ir(piq)3) does not behave as a linear dipole, radiating with lower polarization anisotropy than expected. Spontaneous symmetry breaking occurs in the excited state, leading to a random selection of one of the three ligands to form a charge-transfer state with the metal. This nondeterministic localization is revealed in switching of the degree of linear polarization of phosphorescence. Polarization scrambling likely raises out-coupling efficiency and should be taken into account when deriving molecular orientation of the guest emitter within the OLED host from ensemble angular emission profiles.

  18. Spontaneous fluctuations of transition dipole moment orientation in OLED triplet emitters

    CERN Document Server

    Steiner, Florian; Vogelsang, Jan; Lupton, John M

    2015-01-01

    The efficiency of an organic light-emitting diode (OLED) depends on the microscopic orientation of transition dipole moments of the molecular emitters. The most effective materials used for light generation have threefold symmetry, which prohibit a priori determination of dipole orientation due to the degeneracy of the fundamental transition. Single-molecule spectroscopy reveals that the model triplet emitter tris(2-phenylisoquinoline)iridium(III) (Ir(piq)3) does not behave as a linear dipole, radiating with lower polarization anisotropy than expected. Spontaneous symmetry breaking occurs in the excited state, leading to a random selection of one of the three ligands to form a charge transfer state with the metal. This non-deterministic localization is revealed in switching of the degree of linear polarization of phosphorescence. Polarization scrambling likely raises out-coupling efficiency and should be taken into account when deriving molecular orientation of the guest emitter within the OLED host from ense...

  19. The structure of allophycocyanin B from Synechocystis PCC 6803 reveals the structural basis for the extreme redshift of the terminal emitter in phycobilisomes.

    Science.gov (United States)

    Peng, Pan Pan; Dong, Liang Liang; Sun, Ya Fang; Zeng, Xiao Li; Ding, Wen Long; Scheer, Hugo; Yang, Xiaojing; Zhao, Kai Hong

    2014-10-01

    Allophycocyanin B (AP-B) is one of the two terminal emitters in phycobilisomes, the unique light-harvesting complexes of cyanobacteria and red algae. Its low excitation-energy level and the correspondingly redshifted absorption and fluorescence emission play an important role in funnelling excitation energy from the hundreds of chromophores of the extramembraneous phycobilisome to the reaction centres within the photosynthetic membrane. In the absence of crystal structures of these low-abundance terminal emitters, the molecular basis for the extreme redshift and directional energy transfer is largely unknown. Here, the crystal structure of trimeric AP-B [(ApcD/ApcB)3] from Synechocystis sp. PCC 6803 at 1.75 Å resolution is reported. In the crystal lattice, eight trimers of AP-B form a porous, spherical, 48-subunit assembly of 193 Å in diameter with an internal cavity of 1.1 × 10(6) Å(3). While the overall structure of trimeric AP-B is similar to those reported for many other phycobiliprotein trimers, the chromophore pocket of the α-subunit, ApcD, has more bulky residues that tightly pack the phycocyanobilin (PCB). Ring D of the chromophores is further stabilized by close interactions with ApcB from the adjacent monomer. The combined contributions from both subunits render the conjugated rings B, C and D of the PCB in ApcD almost perfectly coplanar. Together with mutagenesis data, it is proposed that the enhanced planarity effectively extends the conjugation system of PCB and leads to the redshifted absorption (λmax = 669 nm) and fluorescence emission (679 nm) of the ApcD chromophore in AP-B, thereby enabling highly efficient energy transfer from the phycobilisome core to the reaction centres.

  20. Multinozzle Emitter Arrays for Nanoelectrospray Mass Spectrometry

    Energy Technology Data Exchange (ETDEWEB)

    Mao, Pan; Wang, Hung-Ta; Yang, Peidong; Wang, Daojing

    2011-06-16

    Mass spectrometry (MS) is the enabling technology for proteomics and metabolomics. However, dramatic improvements in both sensitivity and throughput are still required to achieve routine MS-based single cell proteomics and metabolomics. Here, we report the silicon-based monolithic multinozzle emitter array (MEA), and demonstrate its proof-of-principle applications in high-sensitivity and high-throughput nanoelectrospray mass spectrometry. Our MEA consists of 96 identical 10-nozzle emitters in a circular array on a 3-inch silicon chip. The geometry and configuration of the emitters, the dimension and number of the nozzles, and the micropillar arrays embedded in the main channel, can be systematically and precisely controlled during the microfabrication process. Combining electrostatic simulation and experimental testing, we demonstrated that sharpened-end geometry at the stem of the individual multinozzle emitter significantly enhanced the electric fields at its protruding nozzle tips, enabling sequential nanoelectrospray for the high-density emitter array. We showed that electrospray current of the multinozzle emitter at a given total flow rate was approximately proportional to the square root of the number of its spraying-nozzles, suggesting the capability of high MS sensitivity for multinozzle emitters. Using a conventional Z-spray mass spectrometer, we demonstrated reproducible MS detection of peptides and proteins for serial MEA emitters, achieving sensitivity and stability comparable to the commercial capillary emitters. Our robust silicon-based MEA chip opens up the possibility of a fully-integrated microfluidic system for ultrahigh-sensitivity and ultrahigh-throughput proteomics and metabolomics.

  1. Emitters of N-photon bundles.

    Science.gov (United States)

    Muñoz, C Sánchez; Del Valle, E; Tudela, A González; Müller, K; Lichtmannecker, S; Kaniber, M; Tejedor, C; Finley, J J; Laussy, F P

    2014-07-01

    Controlling the ouput of a light emitter is one of the basic tasks of photonics, with landmarks such as the laser and single-photon sources. The development of quantum applications makes it increasingly important to diversify the available quantum sources. Here, we propose a cavity QED scheme to realize emitters that release their energy in groups, or "bundles" of N photons, for integer N. Close to 100% of two-photon emission and 90% of three-photon emission is shown to be within reach of state of the art samples. The emission can be tuned with system parameters so that the device behaves as a laser or as a N-photon gun. The theoretical formalism to characterize such emitters is developed, with the bundle statistics arising as an extension of the fundamental correlation functions of quantum optics. These emitters will be useful for quantum information processing and for medical applications.

  2. Adult mouse cortical cell taxonomy revealed by single cell transcriptomics.

    Science.gov (United States)

    Tasic, Bosiljka; Menon, Vilas; Nguyen, Thuc Nghi; Kim, Tae Kyung; Jarsky, Tim; Yao, Zizhen; Levi, Boaz; Gray, Lucas T; Sorensen, Staci A; Dolbeare, Tim; Bertagnolli, Darren; Goldy, Jeff; Shapovalova, Nadiya; Parry, Sheana; Lee, Changkyu; Smith, Kimberly; Bernard, Amy; Madisen, Linda; Sunkin, Susan M; Hawrylycz, Michael; Koch, Christof; Zeng, Hongkui

    2016-02-01

    Nervous systems are composed of various cell types, but the extent of cell type diversity is poorly understood. We constructed a cellular taxonomy of one cortical region, primary visual cortex, in adult mice on the basis of single-cell RNA sequencing. We identified 49 transcriptomic cell types, including 23 GABAergic, 19 glutamatergic and 7 non-neuronal types. We also analyzed cell type-specific mRNA processing and characterized genetic access to these transcriptomic types by many transgenic Cre lines. Finally, we found that some of our transcriptomic cell types displayed specific and differential electrophysiological and axon projection properties, thereby confirming that the single-cell transcriptomic signatures can be associated with specific cellular properties.

  3. The DIORAMA Neutron Emitter

    Energy Technology Data Exchange (ETDEWEB)

    Terry, James Russell [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2016-05-05

    Emission of neutrons in a given event is modeled by the DioramaEmitterNeutron object, a subclass of the abstract DioramaEmitterModule object. The GenerateEmission method of this object is the entry point for generation of a neutron population for a given event. Shown in table 1, this method requires a number of parameters to be defined in the event definition.

  4. The effects of emitter-tied field plates on lateral PNP ionizing radiation response

    Energy Technology Data Exchange (ETDEWEB)

    Barnaby, H.J.; Schrimpf, R.D.; Cirba, C.R. [Vanderbilt Univ., Nashville, TN (United States); Pease, R.L. [RLP Research, Inc., Albuquerque, NM (United States); Fleetwood, D.M. [Sandia National Labs., Albuquerque, NM (United States); Kosier, S.L. [VTC Inc., Bloomington, MN (United States)

    1998-03-01

    Radiation response comparisons of lateral PNP bipolar technologies reveal that device hardening may be achieved by extending the emitter contact over the active base. The emitter-tied field plate suppresses recombination of carriers with interface traps.

  5. Mechanical Properties of Single Collagen Fibrils Revealed by Force Spectroscopy

    Science.gov (United States)

    Graham, John; Phillips, Charlotte; Grandbois, Michel

    2004-03-01

    In the field of biomechanics, collagen fibrils are believed to be robust mechanical structures characterized by a low extensibility. Until very recently, information on the mechanical properties of collagen fibrils could only be derived from ensemble measurements performed on complete tissues such as bone, skin and tendon. Here we measure force-elongation/relaxation profiles of single collagen fibrils using atomic force microscopy-based force spectroscopy. The elongation profiles indicate that in vitro assembled heterotrimeric type I collagen fibrils are characterized by a large extensibility. Numerous discontinuities and a plateau in the force profile indicate major reorganization occurs within the fibrils in the 1.5 -- 4.5 nN range. Our study demonstrates that newly assembled collagen fibrils are robust structures with a significant reserve of elasticity that could play a determinant role in cellular motion in the context of tissue growth and morphogenesis. In contrast, homotrimeric collagen fibrils corresponding to osteogenesis imperfecta pathology exhibit a marked difference in their elasticity profile.

  6. Mesa-top quantum dot single photon emitter arrays: Growth, optical characteristics, and the simulated optical response of integrated dielectric nanoantenna-waveguide systems

    Science.gov (United States)

    Zhang, Jiefei; Chattaraj, Swarnabha; Lu, Siyuan; Madhukar, Anupam

    2016-12-01

    Nanophotonic quantum information processing systems require spatially ordered, spectrally uniform single photon sources (SPSs) integrated on-chip with co-designed light manipulating elements providing emission rate enhancement, emitted photon guidance, and lossless propagation. Towards this goal, we consider systems comprising an SPS array with each SPS coupled to a dielectric building block (DBB) based multifunctional light manipulation unit (LMU). For the SPS array, we report triggered single photon emission from GaAs(001)/InGaAs single quantum dots grown selectively on top of nanomesas using the approach of substrate-encoded size-reducing epitaxy (SESRE). Systematic temperature and power dependent photoluminescence (PL), PL excitation, time-resolved PL, and emission statistics studies reveal high spectral uniformity and single photon emission at 8 K with g(2)(0) of 0.19 ± 0.03. The SESRE based SPS arrays, following growth of a planarizing overlayer, are readily integrable with LMUs fabricated subsequently using either the 2D photonic crystal approach or, as theoretically examined here, DBB based LMUs. We report the simulated optical response of SPS embedded in DBB based nanoantenna-waveguide structures as the multifunctional LMU. The multiple functions of emission rate enhancement, guiding, and lossless propagation are derived from the behavior of the same collective Mie resonance (dominantly magnetic) of the interacting DBB based LMU tuned to the SPS targeted emission wavelength of 980 nm. The simulation utilizes an analytical approach that provides physical insight into the obtained numerical results. Together, the combined experimental and modelling demonstrations open a rich approach to implementing co-designed on-chip integrated SPS-LMUs that, in turn, serve as basic elements of integrated nanophotonic information processing systems.

  7. Homogeneous vs heterogeneous polymerization catalysis revealed by single-particle fluorescence microscopy.

    Science.gov (United States)

    Esfandiari, N Melody; Blum, Suzanne A

    2011-11-16

    A high-sensitivity and high-resolution single-particle fluorescence microscopy technique differentiated between homogeneous and heterogeneous metathesis polymerization catalysis by imaging the location of the early stages of polymerization. By imaging single polymers and single crystals of Grubbs II, polymerization catalysis was revealed to be solely homogeneous rather than heterogeneous or both.

  8. Disentangling the effects of nanoscale structural variations on the light emission wavelength of single nano-emitters: InGaN/GaN multiquantum well nano-LEDs for a case study.

    Science.gov (United States)

    Sarau, George; Heilmann, Martin; Latzel, Michael; Christiansen, Silke

    2014-10-21

    The scattering in the light emission wavelength of semiconductor nano-emitters assigned to nanoscale variations in strain, thickness, and composition is critical in current and novel nanotechnologies from highly efficient light sources to photovoltaics. Here, we present a correlated experimental and theoretical study of single nanorod light emitting diodes (nano-LEDs) based on InGaN/GaN multiquantum wells to separate the contributions of these intrinsic fluctuations. Cathodoluminescence measurements show that nano-LEDs with identical strain states probed by non-resonant micro-Raman spectroscopy can radiate light at different wavelengths. The deviations in the measured optical transitions agree very well with band profile calculations for quantum well thicknesses of 2.07-2.72 nm and In fractions of 17.5-19.5% tightly enclosing the growth values. The nanorod surface roughness controls the appearance of surface optical phonon modes with direct implications on the design of phonon assisted nano-LED devices. This work establishes a new, simple, and powerful methodology for fundamental understanding as well as quantitative analysis of the strain - light emission relationship and surface-related phenomena in the emerging field of nano-emitters.

  9. Microlensless interdigitated photoconductive terahertz emitters.

    Science.gov (United States)

    Singh, Abhishek; Prabhu, S S

    2015-01-26

    We report here fabrication of interdigitated photoconductive antenna (iPCA) terahertz (THz) emitters based on plasmonic electrode design. Novel design of this iPCA enables it to work without microlens array focusing, which is otherwise required for photo excitation of selective photoconductive regions to avoid the destructive interference of emitted THz radiation from oppositely biased regions. Benefit of iPCA over single active region PCA is, photo excitation can be done at larger area hence avoiding the saturation effect at higher optical excitation density. The emitted THz radiation power from plasmonic-iPCAs is ~2 times more than the single active region plasmonic PCA at 200 mW optical excitation, which will further increase at higher optical powers. This design is expected to reduce fabrication cost of photoconductive THz sources and detectors.

  10. Design principles of natural light-harvesting as revealed by single molecule spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Krüger, T.P.J., E-mail: tjaart.kruger@up.ac.za [Department of Physics, University of Pretoria, Private bag X20, Hatfield 0028 (South Africa); Grondelle, R. van [Department of Physics and Astronomy, VU University Amsterdam, De Boelelaan 1081, 1081 HV Amsterdam (Netherlands)

    2016-01-01

    Biology offers a boundless source of adaptation, innovation, and inspiration. A wide range of photosynthetic organisms exist that are capable of harvesting solar light in an exceptionally efficient way, using abundant and low-cost materials. These natural light-harvesting complexes consist of proteins that strongly bind a high density of chromophores to capture solar photons and rapidly transfer the excitation energy to the photochemical reaction centre. The amount of harvested light is also delicately tuned to the level of solar radiation to maintain a constant energy throughput at the reaction centre and avoid the accumulation of the products of charge separation. In this Review, recent developments in the understanding of light-harvesting by plants will be discussed, based on results obtained from single molecule spectroscopy studies. Three design principles of the main light-harvesting antenna of plants will be highlighted: (a) fine, photoactive control over the intrinsic protein disorder to efficiently use intrinsically available thermal energy dissipation mechanisms; (b) the design of the protein microenvironment of a low-energy chromophore dimer to control the amount of shade absorption; (c) the design of the exciton manifold to ensure efficient funneling of the harvested light to the terminal emitter cluster.

  11. Carbon Nanotube Field Emitters

    OpenAIRE

    Zhbanov, Alexander; Pogorelov, Evgeny; Chang, Yia-Chung

    2010-01-01

    In this chapter we theoretically investigate the field emission from carbon nanotube field emitters in diode configuration between a flat anode and cathode. Exact analytical formulas of the electrical field, field enhancement factor, ponderomotive force, and field emission current are found. Applied voltage, height of the needle, radius of curvature on its top, and the work function are the parameters at our disposal. The field enhancement factor, total force and emission current, as well as ...

  12. Power flow from a dipole emitter near an optical antenna.

    Science.gov (United States)

    Huang, Kevin C Y; Jun, Young Chul; Seo, Min-Kyo; Brongersma, Mark L

    2011-09-26

    Current methods to calculate the emission enhancement of a quantum emitter coupled to an optical antenna of arbitrary geometry rely on analyzing the total Poynting vector power flow out of the emitter or the dyadic Green functions from full-field numerical simulations. Unfortunately, these methods do not provide information regarding the nature of the dominant energy decay pathways. We present a new approach that allows for a rigorous separation, quantification, and visualization of the emitter output power flow captured by an antenna and the subsequent reradiation power flow to the far field. Such analysis reveals unprecedented details of the emitter/antenna coupling mechanisms and thus opens up new design strategies for strongly interacting emitter/antenna systems used in sensing, active plasmonics and metamaterials, and quantum optics.

  13. Monolithic multinozzle emitters for nanoelectrospray mass spectrometry

    Science.gov (United States)

    Wang, Daojing; Yang, Peidong; Kim, Woong; Fan, Rong

    2011-09-20

    Novel and significantly simplified procedures for fabrication of fully integrated nanoelectrospray emitters have been described. For nanofabricated monolithic multinozzle emitters (NM.sup.2 emitters), a bottom up approach using silicon nanowires on a silicon sliver is used. For microfabricated monolithic multinozzle emitters (M.sup.3 emitters), a top down approach using MEMS techniques on silicon wafers is used. The emitters have performance comparable to that of commercially-available silica capillary emitters for nanoelectrospray mass spectrometry.

  14. Method of manufacturing a hybrid emitter all back contact solar cell

    Energy Technology Data Exchange (ETDEWEB)

    Loscutoff, Paul; Rim, Seung

    2017-02-07

    A method of manufacturing an all back contact solar cell which has a hybrid emitter design. The solar cell has a thin dielectric layer formed on a backside surface of a single crystalline silicon substrate. One emitter of the solar cell is made of doped polycrystalline silicon that is formed on the thin dielectric layer. A second emitter of the solar cell is formed in the single crystalline silicon substrate and is made of doped single crystalline silicon. The method further includes forming contact holes that allow metal contacts to connect to corresponding emitters.

  15. Courant-Snyder invariant density screening method for emittance analysis

    Institute of Scientific and Technical Information of China (English)

    SUN Ji-Lei; TANG Jing-Yu; JING Han-Tao

    2011-01-01

    Emittance is an important characteristic of describing charged particle beams.In hadron accelerators,we often meet irregular beam distributions that are not appropriately described by a single rms emittance or 95% emittance or total emittance.In this paper,it is pointed out that in many cases a beam halo should be described with very different Courant-Snyder parameters from the ones used for the beam core.A new method - the Courant-Snyder invariant density screening method - is introduced for analyzing emittance data clearly and accurately.The method treats the emittance data from both measurements and numerical simulations.The method uses the statistical distribution of the beam around each particle in phase space to mark its local density parameter,and then uses the density distribution to calculate the beam parameters such as the Courant-Snyder parameters and emittance for different beam boundary definitions.The method has been used in the calculations for.beams from different sources,and shows its advantages over other methods.An application code based on the method including the graphic interface has also been designed.

  16. Single-Molecule Kinetics of λ Exonuclease Reveal Base Dependence and Dynamic Disorder

    NARCIS (Netherlands)

    Oijen, Antoine M. van; Blainey, Paul C.; Crampton, Donald J.; Richardson, Charles C.; Ellenberger, Tom; Xie, X. Sunney

    2003-01-01

    We used a multiplexed approach based on flow-stretched DNA to monitor the enzymatic digestion of λ-phage DNA by individual bacteriophage λ exonuclease molecules. Statistical analyses of multiple single-molecule trajectories observed simultaneously reveal that the catalytic rate is dependent on the l

  17. Global absolute quantification reveals tight regulation of protein expression in single Xenopus eggs.

    Science.gov (United States)

    Smits, Arne H; Lindeboom, Rik G H; Perino, Matteo; van Heeringen, Simon J; Veenstra, Gert Jan C; Vermeulen, Michiel

    2014-09-01

    While recent developments in genomic sequencing technology have enabled comprehensive transcriptome analyses of single cells, single cell proteomics has thus far been restricted to targeted studies. Here, we perform global absolute protein quantification of fertilized Xenopus laevis eggs using mass spectrometry-based proteomics, quantifying over 5800 proteins in the largest single cell proteome characterized to date. Absolute protein amounts in single eggs are highly consistent, thus indicating a tight regulation of global protein abundance. Protein copy numbers in single eggs range from tens of thousands to ten trillion copies per cell. Comparison between the single-cell proteome and transcriptome reveal poor expression correlation. Finally, we identify 439 proteins that significantly change in abundance during early embryogenesis. Downregulated proteins include ribosomal proteins and upregulated proteins include basal transcription factors, among others. Many of these proteins do not show regulation at the transcript level. Altogether, our data reveal that the transcriptome is a poor indicator of the proteome and that protein levels are tightly controlled in X. laevis eggs.

  18. Progress on the emitter wrap-through silicon solar cell

    Science.gov (United States)

    Gee, J. M.; Buck, M. E.; Schubert, W. K.; Basore, P. A.

    The Emitter Wrap-Through (EWT) solar cell is a back-contacted solar cell with a carrier-collection junction (emitter) on the front surface. Elimination of grids from the front surface allows for higher performance by eliminating grid-obscuration losses and reducing series resistance, while keeping an emitter on the front surface maintains high collection efficiency in solar-grade materials with modest diffusion lengths. The EWT cell uses laser-drilled vias to wrap the emitter diffusion on the front surface to interdigitated contacts on the back surface. We report on progress towards demonstration of two concepts for the EWT cell. The first EWT concept uses a fabrication sequence based on heavily diffused grooves and plated metallizations, and the second EWT concept uses a single furnace step and screen-printed metallizations. We also report on demonstration of double-sided carrier collection in the EWT cell.

  19. Design rules for core/shell nanowire resonant emitters

    Science.gov (United States)

    Kim, Da-Som; Kim, Sun-Kyung

    2017-01-01

    We study design principles to boost the extraction of light from core/shell GaN nanowire optical emitters. A full-vectorial electromagnetic simulation reveals that the extraction efficiency of an emitter within a nanowire cavity depends strongly on its position; the efficiency becomes maximized as the emitter's location approaches the center of the structure. The total extraction of light is sinusoidally modulated by the nanowire diameter, which is directly correlated with optical resonances. The introduction of a conformal dielectric coating on a nanowire leads to a dramatic enhancement in the extraction efficiency, which results from an increase in side emission owing to an optical antenna effect. A simple high-refractive-index dielectric coating approximately doubles the total extraction efficiency of a nanowire LED. These numerical findings will be valuable in providing strategies for high-efficiency nanowire-based optical emitters.

  20. Single-atom coherent field electron emitters for practical application to electron microscopy: Buildup controllability, self-repairing function and demountable characteristic

    Energy Technology Data Exchange (ETDEWEB)

    Rokuta, E. [Institute for Material Science and Technologies, Waseda University, 2-8-26 Nishiwaseda, Shinjuku, Tokyo 169-0051 (Japan)]. E-mail: rokuta@waseda.jp; Itagaki, T. [Institute for Material Science and Technologies, Waseda University, 2-8-26 Nishiwaseda, Shinjuku, Tokyo 169-0051 (Japan); Ishikawa, T. [Institute for Material Science and Technologies, Waseda University, 2-8-26 Nishiwaseda, Shinjuku, Tokyo 169-0051 (Japan); Cho, B.-L. [Institute for Material Science and Technologies, Waseda University, 2-8-26 Nishiwaseda, Shinjuku, Tokyo 169-0051 (Japan); Kuo, H.-S. [Institute of Physics, Academia Sinica, Nankang, Taipei, Taiwan (China); Tsong, T.T. [Institute of Physics, Academia Sinica, Nankang, Taipei, Taiwan (China); Oshima, C. [Institute for Material Science and Technologies, Waseda University, 2-8-26 Nishiwaseda, Shinjuku, Tokyo 169-0051 (Japan)

    2006-03-15

    We have fabricated single-atom field emission (FE) tips by annealing Rh-deposited W tips at 900 K, and the FE characteristics were investigated. Due to the formation of the nanotips, the electron beams were confined in a semi-cone angle of 3 deg., an indication quite different from the conventional FE beams. In repairing-function test where the FE nanotips were intentionally destroyed beforehand, they recovered the peculiar FE characteristics by means of feasible low temperature annealing. Finally, we found that the present nanotips equipped the capability of recovering the unique FE properties even after an exposure to the air. These characteristics are significantly relevant to the practical applications to electron-optics instruments.

  1. Warm-white light-emitting diode with high color rendering index fabricated by combining trichromatic InGaN emitter with single red phosphor.

    Science.gov (United States)

    Sheu, Jinn-Kong; Chen, Fu-Bang; Wang, Yen-Chin; Chang, Chih-Chiang; Huang, Shih-Hsien; Liu, Chun-Nan; Lee, Ming-Lun

    2015-04-06

    We present a trichromatic GaN-based light-emitting diode (LED) that emits near-ultraviolet (n-UV) blue and green peaks combined with red phosphor to generate white light with a low correlated color temperature (CCT) and high color rendering index (CRI). The LED structure, blue and green unipolar InGaN/GaN multiple quantum wells (MQWs) stacked with a top p-i-n structure containing an InGaN/GaN MQW emitting n-UV light, was grown epitaxially on a single substrate. The trichromatic LED chips feature a vertical conduction structure on a silicon substrate fabricated through wafer bonding and laser lift-off techniques. The blue and green InGaN/GaN MQWs were pumped with n-UV light to re-emit low-energy photons when the LEDs were electrically driven with a forward current. The emission spectrum included three peaks at approximately 405, 468, and 537 nm. Furthermore, the trichromatic LED chips were combined with red phosphor to generate white light with a CCT and CRI of approximately 2900 and 92, respectively.

  2. The heterogeneity of human CD127(+) innate lymphoid cells revealed by single-cell RNA sequencing.

    Science.gov (United States)

    Björklund, Åsa K; Forkel, Marianne; Picelli, Simone; Konya, Viktoria; Theorell, Jakob; Friberg, Danielle; Sandberg, Rickard; Mjösberg, Jenny

    2016-04-01

    Innate lymphoid cells (ILCs) are increasingly appreciated as important participants in homeostasis and inflammation. Substantial plasticity and heterogeneity among ILC populations have been reported. Here we have delineated the heterogeneity of human ILCs through single-cell RNA sequencing of several hundreds of individual tonsil CD127(+) ILCs and natural killer (NK) cells. Unbiased transcriptional clustering revealed four distinct populations, corresponding to ILC1 cells, ILC2 cells, ILC3 cells and NK cells, with their respective transcriptomes recapitulating known as well as unknown transcriptional profiles. The single-cell resolution additionally divulged three transcriptionally and functionally diverse subpopulations of ILC3 cells. Our systematic comparison of single-cell transcriptional variation within and between ILC populations provides new insight into ILC biology during homeostasis, with additional implications for dysregulation of the immune system.

  3. Fully tuneable, Purcell-enhanced solid-state quantum emitters

    Energy Technology Data Exchange (ETDEWEB)

    Petruzzella, M., E-mail: m.petruzzella@tue.nl; Xia, T.; Pagliano, F.; Birindelli, S.; Zobenica, Z.; Fiore, A. [COBRA Research Institute, Eindhoven University of Technology, P.O. Box 513, NL-5600MB Eindhoven (Netherlands); Midolo, L. [Niels Bohr Institute, University of Copenhagen, Blegdamsvej 17, DK-2100 Copenhagen (Denmark); Li, L. H.; Linfield, E. H. [School of Electronic and Electrical Engineering, University of Leeds, Leeds LS2 9JT (United Kingdom)

    2015-10-05

    We report the full energy control over a semiconductor cavity-emitter system, consisting of single Stark-tunable quantum dots embedded in mechanically reconfigurable photonic crystal membranes. A reversible wavelength tuning of the emitter over 7.5 nm as well as an 8.5 nm mode shift are realized on the same device. Harnessing these two electrical tuning mechanisms, a single exciton transition is brought on resonance with the cavity mode at several wavelengths, demonstrating a ten-fold enhancement of its spontaneous emission. These results open the way to bring several cavity-enhanced emitters mutually into resonance and therefore represent a key step towards scalable quantum photonic circuits featuring multiple sources of indistinguishable single photons.

  4. Single-molecule chemical reaction reveals molecular reaction kinetics and dynamics.

    Science.gov (United States)

    Zhang, Yuwei; Song, Ping; Fu, Qiang; Ruan, Mingbo; Xu, Weilin

    2014-06-25

    Understanding the microscopic elementary process of chemical reactions, especially in condensed phase, is highly desirable for improvement of efficiencies in industrial chemical processes. Here we show an approach to gaining new insights into elementary reactions in condensed phase by combining quantum chemical calculations with a single-molecule analysis. Elementary chemical reactions in liquid-phase, revealed from quantum chemical calculations, are studied by tracking the fluorescence of single dye molecules undergoing a reversible redox process. Statistical analyses of single-molecule trajectories reveal molecular reaction kinetics and dynamics of elementary reactions. The reactivity dynamic fluctuations of single molecules are evidenced and probably arise from either or both of the low-frequency approach of the molecule to the internal surface of the SiO2 nanosphere or the molecule diffusion-induced memory effect. This new approach could be applied to other chemical reactions in liquid phase to gain more insight into their molecular reaction kinetics and the dynamics of elementary steps.

  5. Beta emitters and radiation protection

    DEFF Research Database (Denmark)

    Jødal, Lars

    2009-01-01

    , and 90Y, using data from a freely available database. Bremsstrahlung yields were calculated for 90Y shielded by lead, aluminium, or perspex. Bremsstrahlung spectrum from 90Y shielded by perspex was measured, and attenuation of spectrum by lead was calculated. Whole-body and finger doses to persons...... preparing 90Y-Zevalin were measured. CONCLUSIONS. Good laboratory practice is important to keep radiation doses low. To reduce bremsstrahlung, 90Y should not be shielded by lead but instead perspex (10 mm) or aluminium (5 mm). Bremsstrahlung radiation can be further reduced by adding a millimetre of lead......BACKGROUND. Beta emitters, such as 90Y, are increasingly being used for cancer treatment. However, beta emitters demand other precautions than gamma emitters during preparation and administration, especially concerning shielding. AIM. To discuss practical precautions for handling beta emitters...

  6. Visible Spectrum Incandescent Selective Emitter

    Energy Technology Data Exchange (ETDEWEB)

    Sonsight Inc.

    2004-04-30

    The purpose of the work performed was to demonstrate the feasibility of a novel bi-layer selective emitter. Selective emitters are incandescent radiant bodies with emissivities that are substantially larger in a selected part of the radiation spectrum, thereby significantly shifting their radiated spectral distribution from that of a blackbody radiating at the same temperature. The major research objectives involved answering the following questions: (1) What maximum VIS/NIR radiant power and emissivity ratios can be attained at 2650 K? (2) What is the observed emitter body life and how does its performance vary with time? (3) What are the design tradeoffs for a dual heating approach in which both an internally mounted heating coil and electrical resistance self-heating are used? (4) What are the quantitative improvements to be had from utilizing a bi-layer emitter body with a low emissivity inner layer and a partially transmissive outer layer? Two approaches to obtaining selective emissivity were investigated. The first was to utilize large optical scattering within an emitter material with a spectral optical absorption that is much greater within the visible spectrum than that within the NIR. With this approach, an optically thick emitter can radiate almost as if optically thin because essentially, scattering limits the distance below the surface from which significant amounts of internally generated radiation can emerge. The performance of thin emitters was also investigated (for optically thin emitters, spectral emissivity is proportional to spectral absorptivity). These emitters were fabricated from thin mono-layer emitter rods as well as from bi-layer rods with a thin emitter layer mounted on a substrate core. With an initially estimated energy efficiency of almost three times that of standard incandescent bulbs, a number of energy, economic and environmental benefits such as less energy use and cost, reduced CO{sub 2} emissions, and no mercury contamination

  7. Revealing −1 Programmed Ribosomal Frameshifting Mechanisms by Single-Molecule Techniques and Computational Methods

    Directory of Open Access Journals (Sweden)

    Kai-Chun Chang

    2012-01-01

    Full Text Available Programmed ribosomal frameshifting (PRF serves as an intrinsic translational regulation mechanism employed by some viruses to control the ratio between structural and enzymatic proteins. Most viral mRNAs which use PRF adapt an H-type pseudoknot to stimulate −1 PRF. The relationship between the thermodynamic stability and the frameshifting efficiency of pseudoknots has not been fully understood. Recently, single-molecule force spectroscopy has revealed that the frequency of −1 PRF correlates with the unwinding forces required for disrupting pseudoknots, and that some of the unwinding work dissipates irreversibly due to the torsional restraint of pseudoknots. Complementary to single-molecule techniques, computational modeling provides insights into global motions of the ribosome, whose structural transitions during frameshifting have not yet been elucidated in atomic detail. Taken together, recent advances in biophysical tools may help to develop antiviral therapies that target the ubiquitous −1 PRF mechanism among viruses.

  8. Structural dynamics of potassium-channel gating revealed by single-molecule FRET.

    Science.gov (United States)

    Wang, Shizhen; Vafabakhsh, Reza; Borschel, William F; Ha, Taekjip; Nichols, Colin G

    2016-01-01

    Crystallography has provided invaluable insights regarding ion-channel selectivity and gating, but to advance understanding to a new level, dynamic views of channel structures within membranes are essential. We labeled tetrameric KirBac1.1 potassium channels with single donor and acceptor fluorophores at different sites and then examined structural dynamics within lipid membranes by single-molecule fluorescence resonance energy transfer (FRET). We found that the extracellular region is structurally rigid in both closed and open states, whereas the N-terminal slide helix undergoes marked conformational fluctuations. The cytoplasmic C-terminal domain fluctuates between two major structural states, both of which become less dynamic and move away from the pore axis and away from the membrane in closed channels. Our results reveal mobile and rigid conformations of functionally relevant KirBac1.1 channel motifs, implying similar dynamics for similar motifs in eukaryotic Kir channels and in cation channels in general.

  9. Structural dynamics of potassium channel gating revealed by single molecule FRET

    Science.gov (United States)

    Borschel, William F.; Ha, Taekjip; Nichols, Colin G.

    2016-01-01

    Crystallography has provided invaluable insights to ion channel selectivity and gating, but to advance understanding to a new level, dynamic views of channel structures within membranes are essential. We labeled tetrameric KirBac1.1 potassium channels with single donor and acceptor fluorophores at different sites, and examined structural dynamics within lipid membranes by single molecule FRET. We found that the extracellular region is structurally rigid in both closed and open states, whereas the N-terminal slide helix undergoes marked conformational fluctuations. The cytoplasmic C-terminal domain fluctuates between two major structural states both of which become less dynamic and move away from the pore axis and away from the membrane in closed channels. Our results reveal mobile and rigid conformations of functionally relevant KirBac1.1 channel motifs, implying similar dynamics for similar motifs in eukaryotic Kir channels and for cation channels in general. PMID:26641713

  10. Quantum Yield Heterogeneity among Single Nonblinking Quantum Dots Revealed by Atomic Structure-Quantum Optics Correlation.

    Science.gov (United States)

    Orfield, Noah J; McBride, James R; Wang, Feng; Buck, Matthew R; Keene, Joseph D; Reid, Kemar R; Htoon, Han; Hollingsworth, Jennifer A; Rosenthal, Sandra J

    2016-02-23

    Physical variations in colloidal nanostructures give rise to heterogeneity in expressed optical behavior. This correlation between nanoscale structure and function demands interrogation of both atomic structure and photophysics at the level of single nanostructures to be fully understood. Herein, by conducting detailed analyses of fine atomic structure, chemical composition, and time-resolved single-photon photoluminescence data for the same individual nanocrystals, we reveal inhomogeneity in the quantum yields of single nonblinking "giant" CdSe/CdS core/shell quantum dots (g-QDs). We find that each g-QD possesses distinctive single exciton and biexciton quantum yields that result mainly from variations in the degree of charging, rather than from volume or structure inhomogeneity. We further establish that there is a very limited nonemissive "dark" fraction (<2%) among the studied g-QDs and present direct evidence that the g-QD core must lack inorganic passivation for the g-QD to be "dark". Therefore, in contrast to conventional QDs, ensemble photoluminescence quantum yield is principally defined by charging processes rather than the existence of dark g-QDs.

  11. Single-molecule spectroscopy reveals photosynthetic LH2 complexes switch between emissive states.

    Science.gov (United States)

    Schlau-Cohen, Gabriela S; Wang, Quan; Southall, June; Cogdell, Richard J; Moerner, W E

    2013-07-01

    Photosynthetic organisms flourish under low light intensities by converting photoenergy to chemical energy with near unity quantum efficiency and under high light intensities by safely dissipating excess photoenergy and deleterious photoproducts. The molecular mechanisms balancing these two functions remain incompletely described. One critical barrier to characterizing the mechanisms responsible for these processes is that they occur within proteins whose excited-state properties vary drastically among individual proteins and even within a single protein over time. In ensemble measurements, these excited-state properties appear only as the average value. To overcome this averaging, we investigate the purple bacterial antenna protein light harvesting complex 2 (LH2) from Rhodopseudomonas acidophila at the single-protein level. We use a room-temperature, single-molecule technique, the anti-Brownian electrokinetic trap, to study LH2 in a solution-phase (nonperturbative) environment. By performing simultaneous measurements of fluorescence intensity, lifetime, and spectra of single LH2 complexes, we identify three distinct states and observe transitions occurring among them on a timescale of seconds. Our results reveal that LH2 complexes undergo photoactivated switching to a quenched state, likely by a conformational change, and thermally revert to the ground state. This is a previously unobserved, reversible quenching pathway, and is one mechanism through which photosynthetic organisms can adapt to changes in light intensities.

  12. Vibrio cholerae biofilm growth program and architecture revealed by single-cell live imaging.

    Science.gov (United States)

    Yan, Jing; Sharo, Andrew G; Stone, Howard A; Wingreen, Ned S; Bassler, Bonnie L

    2016-09-01

    Biofilms are surface-associated bacterial communities that are crucial in nature and during infection. Despite extensive work to identify biofilm components and to discover how they are regulated, little is known about biofilm structure at the level of individual cells. Here, we use state-of-the-art microscopy techniques to enable live single-cell resolution imaging of a Vibrio cholerae biofilm as it develops from one single founder cell to a mature biofilm of 10,000 cells, and to discover the forces underpinning the architectural evolution. Mutagenesis, matrix labeling, and simulations demonstrate that surface adhesion-mediated compression causes V. cholerae biofilms to transition from a 2D branched morphology to a dense, ordered 3D cluster. We discover that directional proliferation of rod-shaped bacteria plays a dominant role in shaping the biofilm architecture in V. cholerae biofilms, and this growth pattern is controlled by a single gene, rbmA Competition analyses reveal that the dense growth mode has the advantage of providing the biofilm with superior mechanical properties. Our single-cell technology can broadly link genes to biofilm fine structure and provides a route to assessing cell-to-cell heterogeneity in response to external stimuli.

  13. Crystal structure of AcrB in complex with a single transmembrane subunit reveals another twist.

    Science.gov (United States)

    Törnroth-Horsefield, Susanna; Gourdon, Pontus; Horsefield, Rob; Brive, Lars; Yamamoto, Natsuko; Mori, Hirotada; Snijder, Arjan; Neutze, Richard

    2007-12-01

    Bacterial drug resistance is a serious concern for human health. Multidrug efflux pumps export a broad variety of substrates out of the cell and thereby convey resistance to the host. In Escherichia coli, the AcrB:AcrA:TolC efflux complex forms a principal transporter for which structures of the individual component proteins have been determined in isolation. Here, we present the X-ray structure of AcrB in complex with a single transmembrane protein, assigned by mass spectrometry as YajC. A specific rotation of the periplasmic porter domain of AcrB is also revealed, consistent with the hypothesized "twist-to-open" mechanism for TolC activation. Growth experiments with yajc-deleted E. coli reveal a modest increase in the organism's susceptibility to beta-lactam antibiotics, but this effect could not conclusively be attributed to the loss of interactions between YajC and AcrB.

  14. Single-Molecule FRET Reveals Hidden Complexity in a Protein Energy Landscape

    OpenAIRE

    Tsytlonok, Maksym; Ibrahim, Shehu M.; Rowling, Pamela J.E.; Xu, Wenshu; Ruedas-Rama, Maria J.; Orte, Angel; Klenerman, David; Itzhaki, Laura S.

    2015-01-01

    Summary Here, using single-molecule FRET, we reveal previously hidden conformations of the ankyrin-repeat domain of AnkyrinR, a giant adaptor molecule that anchors integral membrane proteins to the spectrin-actin cytoskeleton through simultaneous binding of multiple partner proteins. We show that the ankyrin repeats switch between high-FRET and low-FRET states, controlled by an unstructured “safety pin” or “staple” from the adjacent domain of AnkyrinR. Opening of the safety pin leads to unrav...

  15. Single Platform Geolocation of Radio Frequency Emitters

    Science.gov (United States)

    2015-03-26

    determine the AOA of K impinging signals. The M × M spatial covariance matrix is given as [9] Rxx = E [ XXH ] = E [ (AS + W) (AS + W)H ] = AE [ SSH ] AH + E...σ2wIM×M (2.22) and (2.21) becomes Rxx = ARssAH + σ2wIM×M (2.23) where Rss = E [ SSH ] (2.24) is the K × K signal covariance matrix. In the case of zero

  16. Deterministic strain-induced arrays of quantum emitters in a two-dimensional semiconductor

    Science.gov (United States)

    Branny, Artur; Kumar, Santosh; Proux, Raphaël; Gerardot, Brian D

    2017-01-01

    An outstanding challenge in quantum photonics is scalability, which requires positioning of single quantum emitters in a deterministic fashion. Site positioning progress has been made in established platforms including defects in diamond and self-assembled quantum dots, albeit often with compromised coherence and optical quality. The emergence of single quantum emitters in layered transition metal dichalcogenide semiconductors offers new opportunities to construct a scalable quantum architecture. Here, using nanoscale strain engineering, we deterministically achieve a two-dimensional lattice of quantum emitters in an atomically thin semiconductor. We create point-like strain perturbations in mono- and bi-layer WSe2 which locally modify the band-gap, leading to efficient funnelling of excitons towards isolated strain-tuned quantum emitters that exhibit high-purity single photon emission. We achieve near unity emitter creation probability and a mean positioning accuracy of 120±32 nm, which may be improved with further optimization of the nanopillar dimensions. PMID:28530219

  17. Deterministic strain-induced arrays of quantum emitters in a two-dimensional semiconductor

    Science.gov (United States)

    Branny, Artur; Kumar, Santosh; Proux, Raphaël; Gerardot, Brian D.

    2017-05-01

    An outstanding challenge in quantum photonics is scalability, which requires positioning of single quantum emitters in a deterministic fashion. Site positioning progress has been made in established platforms including defects in diamond and self-assembled quantum dots, albeit often with compromised coherence and optical quality. The emergence of single quantum emitters in layered transition metal dichalcogenide semiconductors offers new opportunities to construct a scalable quantum architecture. Here, using nanoscale strain engineering, we deterministically achieve a two-dimensional lattice of quantum emitters in an atomically thin semiconductor. We create point-like strain perturbations in mono- and bi-layer WSe2 which locally modify the band-gap, leading to efficient funnelling of excitons towards isolated strain-tuned quantum emitters that exhibit high-purity single photon emission. We achieve near unity emitter creation probability and a mean positioning accuracy of 120+/-32 nm, which may be improved with further optimization of the nanopillar dimensions.

  18. Multi-omics maps of cotton fibre reveal epigenetic basis for staged single-cell differentiation.

    Science.gov (United States)

    Wang, Maojun; Wang, Pengcheng; Tu, Lili; Zhu, Sitao; Zhang, Lin; Li, Zhonghua; Zhang, Qinghua; Yuan, Daojun; Zhang, Xianlong

    2016-05-19

    Epigenetic modifications are highlighted for their great importance in regulating plant development, but their function associated with single-cell differentiation remains undetermined. Here, we used the cotton fibre, which is the epidermal hair on the cotton ovule, as a model to investigate the regulatory role of DNA methylation in cell differentiation. The level of CHH (H = A, T, or C) DNA methylation level was found to increase during fibre development, accompanied by a decrease in RNA-directed DNA methylation (RdDM). Examination of nucleosome positioning revealed a gradual transition from euchromatin to heterochromatin for chromatin dynamics in developing fibres, which could shape the DNA methylation landscape. The observed increase in DNA methylation in fibres, compared with other ovule tissue, was demonstrated to be mediated predominantly by an active H3K9me2-dependent pathway rather than the RdDM pathway, which was inactive. Furthermore, integrated multi-omics analyses revealed that dynamic DNA methylation played a role in the regulation of lipid biosynthesis and spatio-temporal modulation of reactive oxygen species during fibre differentiation. Our study illustrates two divergent pathways mediating a continuous increase of DNA methylation and also sheds further light on the epigenetic basis for single-cell differentiation in plants. These data and analyses are made available to the wider research community through a comprehensive web portal. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

  19. Revealing nonergodic dynamics in living cells from a single particle trajectory.

    Science.gov (United States)

    Lanoiselée, Yann; Grebenkov, Denis S

    2016-05-01

    We propose the improved ergodicity and mixing estimators to identify nonergodic dynamics from a single particle trajectory. The estimators are based on the time-averaged characteristic function of the increments and can thus capture additional information on the process as compared to the conventional time-averaged mean-square displacement. The estimators are first investigated and validated for several models of anomalous diffusion, such as ergodic fractional Brownian motion and diffusion on percolating clusters, and nonergodic continuous-time random walks and scaled Brownian motion. The estimators are then applied to two sets of earlier published trajectories of mRNA molecules inside live Escherichia coli cells and of Kv2.1 potassium channels in the plasma membrane. These statistical tests did not reveal nonergodic features in the former set, while some trajectories of the latter set could be classified as nonergodic. Time averages along such trajectories are thus not representative and may be strongly misleading. Since the estimators do not rely on ensemble averages, the nonergodic features can be revealed separately for each trajectory, providing a more flexible and reliable analysis of single-particle tracking experiments in microbiology.

  20. Metagenomics, metatranscriptomics and single cell genomics reveal functional response of active Oceanospirillales to Gulf oil spill

    Energy Technology Data Exchange (ETDEWEB)

    Mason, Olivia U.; Hazen, Terry C.; Borglin, Sharon; Chain, Patrick S. G.; Dubinsky, Eric A.; Fortney, Julian L.; Han, James; Holman, Hoi-Ying N.; Hultman, Jenni; Lamendella, Regina; Mackelprang, Rachel; Malfatti, Stephanie; Tom, Lauren M.; Tringe, Susannah G.; Woyke, Tanja; Zhou, Jizhong; Rubin, Edward M.; Jansson, Janet K.

    2012-06-12

    The Deepwater Horizon oil spill in the Gulf of Mexico resulted in a deep-sea hydrocarbon plume that caused a shift in the indigenous microbial community composition with unknown ecological consequences. Early in the spill history, a bloom of uncultured, thus uncharacterized, members of the Oceanospirillales was previously detected, but their role in oil disposition was unknown. Here our aim was to determine the functional role of the Oceanospirillales and other active members of the indigenous microbial community using deep sequencing of community DNA and RNA, as well as single-cell genomics. Shotgun metagenomic and metatranscriptomic sequencing revealed that genes for motility, chemotaxis and aliphatic hydrocarbon degradation were significantly enriched and expressed in the hydrocarbon plume samples compared with uncontaminated seawater collected from plume depth. In contrast, although genes coding for degradation of more recalcitrant compounds, such as benzene, toluene, ethylbenzene, total xylenes and polycyclic aromatic hydrocarbons, were identified in the metagenomes, they were expressed at low levels, or not at all based on analysis of the metatranscriptomes. Isolation and sequencing of two Oceanospirillales single cells revealed that both cells possessed genes coding for n-alkane and cycloalkane degradation. Specifically, the near-complete pathway for cyclohexane oxidation in the Oceanospirillales single cells was elucidated and supported by both metagenome and metatranscriptome data. The draft genome also included genes for chemotaxis, motility and nutrient acquisition strategies that were also identified in the metagenomes and metatranscriptomes. These data point towards a rapid response of members of the Oceanospirillales to aliphatic hydrocarbons in the deep sea.

  1. Coupled electrophysiological recording and single cell transcriptome analyses revealed molecular mechanisms underlying neuronal maturation

    Directory of Open Access Journals (Sweden)

    Xiaoying Chen

    2016-02-01

    Full Text Available ABSTRACT The mammalian brain is heterogeneous, containing billions of neurons and trillions of synapses forming various neural circuitries, through which sense, movement, thought, and emotion arise. The cellular heterogeneity of the brain has made it difficult to study the molecular logic of neural circuitry wiring, pruning, activation, and plasticity, until recently, transcriptome analyses with single cell resolution makes decoding of gene regulatory networks underlying aforementioned circuitry properties possible. Here we report success in performing both electrophysiological and whole-genome transcriptome analyses on single human neurons in culture. Using Weighted Gene Coexpression Network Analyses (WGCNA, we identified gene clusters highly correlated with neuronal maturation judged by electrophysiological characteristics. A tight link between neuronal maturation and genes involved in ubiquitination and mitochondrial function was revealed. Moreover, we identified a list of candidate genes, which could potentially serve as biomarkers for neuronal maturation. Coupled electrophysiological recording and single cell transcriptome analysis will serve as powerful tools in the future to unveil molecular logics for neural circuitry functions.

  2. Ecology of uncultured Prochlorococcus clades revealed through single-cell genomics and biogeographic analysis.

    Science.gov (United States)

    Malmstrom, Rex R; Rodrigue, Sébastien; Huang, Katherine H; Kelly, Libusha; Kern, Suzanne E; Thompson, Anne; Roggensack, Sara; Berube, Paul M; Henn, Matthew R; Chisholm, Sallie W

    2013-01-01

    Prochlorococcus is the numerically dominant photosynthetic organism throughout much of the world's oceans, yet little is known about the ecology and genetic diversity of populations inhabiting tropical waters. To help close this gap, we examined natural Prochlorococcus communities in the tropical Pacific Ocean using a single-cell whole-genome amplification and sequencing. Analysis of the gene content of just 10 single cells from these waters added 394 new genes to the Prochlorococcus pan-genome--that is, genes never before seen in a Prochlorococcus cell. Analysis of marker genes, including the ribosomal internal transcribed sequence, from dozens of individual cells revealed several representatives from two uncultivated clades of Prochlorococcus previously identified as HNLC1 and HNLC2. While the HNLC clades can dominate Prochlorococcus communities under certain conditions, their overall geographic distribution was highly restricted compared with other clades of Prochlorococcus. In the Atlantic and Pacific oceans, these clades were only found in warm waters with low Fe and high inorganic P levels. Genomic analysis suggests that at least one of these clades thrives in low Fe environments by scavenging organic-bound Fe, a process previously unknown in Prochlorococcus. Furthermore, the capacity to utilize organic-bound Fe appears to have been acquired horizontally and may be exchanged among other clades of Prochlorococcus. Finally, one of the single Prochlorococcus cells sequenced contained a partial genome of what appears to be a prophage integrated into the genome.

  3. The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells.

    Science.gov (United States)

    Trapnell, Cole; Cacchiarelli, Davide; Grimsby, Jonna; Pokharel, Prapti; Li, Shuqiang; Morse, Michael; Lennon, Niall J; Livak, Kenneth J; Mikkelsen, Tarjei S; Rinn, John L

    2014-04-01

    Defining the transcriptional dynamics of a temporal process such as cell differentiation is challenging owing to the high variability in gene expression between individual cells. Time-series gene expression analyses of bulk cells have difficulty distinguishing early and late phases of a transcriptional cascade or identifying rare subpopulations of cells, and single-cell proteomic methods rely on a priori knowledge of key distinguishing markers. Here we describe Monocle, an unsupervised algorithm that increases the temporal resolution of transcriptome dynamics using single-cell RNA-Seq data collected at multiple time points. Applied to the differentiation of primary human myoblasts, Monocle revealed switch-like changes in expression of key regulatory factors, sequential waves of gene regulation, and expression of regulators that were not known to act in differentiation. We validated some of these predicted regulators in a loss-of function screen. Monocle can in principle be used to recover single-cell gene expression kinetics from a wide array of cellular processes, including differentiation, proliferation and oncogenic transformation.

  4. Combustion powered thermophotovoltaic emitter system

    Energy Technology Data Exchange (ETDEWEB)

    McHenry, R.S. [Naval Academy, Annapolis, MD (United States). Naval Architecture, Ocean and Marine Engineering

    1995-07-01

    The US Naval Academy (USNA) has recently completed an engineering design project for a high temperature thermophotovoltaic (TPV) photon emitter. The final apparatus was to be portable, completely self contained, and was to incorporate cycle efficiency optimization such as exhaust stream recuperation. Through computer modeling and prototype experimentation, a methane fueled emitter system was designed from structural ceramic materials to fulfill the high temperature requirements necessary for high system efficiency. This paper outlines the engineering design process, discusses obstacles and solutions encountered, and presents the final design.

  5. Single-molecule force spectroscopy reveals the individual mechanical unfolding pathways of a surface layer protein.

    Science.gov (United States)

    Horejs, Christine; Ristl, Robin; Tscheliessnig, Rupert; Sleytr, Uwe B; Pum, Dietmar

    2011-08-05

    Surface layers (S-layers) represent an almost universal feature of archaeal cell envelopes and are probably the most abundant bacterial cell proteins. S-layers are monomolecular crystalline structures of single protein or glycoprotein monomers that completely cover the cell surface during all stages of the cell growth cycle, thereby performing their intrinsic function under a constant intra- and intermolecular mechanical stress. In gram-positive bacteria, the individual S-layer proteins are anchored by a specific binding mechanism to polysaccharides (secondary cell wall polymers) that are linked to the underlying peptidoglycan layer. In this work, atomic force microscopy-based single-molecule force spectroscopy and a polyprotein approach are used to study the individual mechanical unfolding pathways of an S-layer protein. We uncover complex unfolding pathways involving the consecutive unfolding of structural intermediates, where a mechanical stability of 87 pN is revealed. Different initial extensibilities allow the hypothesis that S-layer proteins adapt highly stable, mechanically resilient conformations that are not extensible under the presence of a pulling force. Interestingly, a change of the unfolding pathway is observed when individual S-layer proteins interact with secondary cell wall polymers, which is a direct signature of a conformational change induced by the ligand. Moreover, the mechanical stability increases up to 110 pN. This work demonstrates that single-molecule force spectroscopy offers a powerful tool to detect subtle changes in the structure of an individual protein upon binding of a ligand and constitutes the first conformational study of surface layer proteins at the single-molecule level.

  6. Ultra-Sensitivity Glucose Sensor Based on Field Emitters

    Directory of Open Access Journals (Sweden)

    Song Yinglin

    2009-01-01

    Full Text Available Abstract A new glucose sensor based on field emitter of ZnO nanorod arrays (ZNA was fabricated. This new type of ZNA field emitter-based sensor shows high sensitivity with experimental limit of detection of 1 nM glucose solution and a detection range from 1 nM to 50 μM in air at room temperature, which is lower than that of glucose sensors based on surface plasmon resonance spectroscopy, fluorescence signal transmission, and electrochemical signal transduction. The new glucose sensor provides a key technique for promising consuming application in biological system for detecting low levels of glucose on single cells or bacterial cultures.

  7. Copper conducting electrode with nickel as a seed layer for selective emitter crystalline silicon solar cells

    Energy Technology Data Exchange (ETDEWEB)

    Rehman, Atteq ur; Shin, Eun Gu; Lee, Soo Hong [Sejong University, Seoul (Korea, Republic of)

    2014-09-15

    In this research, we investigated selective emitter formation with a single-step photolithography process having a metallization scheme composed of nickel/copper metal stacks. The nickel seed layers were deposited by applying the electroless deposition process while copper was formed by light induced electro-plating arrangements as the main conducting electrode. The electroless deposition of nickel, along with a sintering process, was employed to create a diffusion barrier between copper and silicon. The nickel metal stack below the copper-conducting electrode also helped in lowering the sheet resistance and improving the contact adhesion. The nickel used as a seed layer was successfully demonstrated in the fabrication of a homogeneous 60 Ω/ emitter and selective emitter cells. Lower series resistances of 0.165 Ω and 0.253 Ω were achieved for the selective emitter and the homogeneous emitter cells, respectively. The best cell efficiency of 18.37% for the selective emitter solar cell was achieved, with average cell efficiencies of 18.17% and 17.3% for the selective emitter and the homogeneous emitter cells, respectively. An approximate efficiency increase of about 0.8% was recorded for the selective emitter solar cells.

  8. Elementary framework for cold field emission from quantum-confined, non-planar emitters

    Energy Technology Data Exchange (ETDEWEB)

    Patterson, A. A., E-mail: apatters@mit.edu; Akinwande, A. I. [Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA and Microsystems Technology Laboratories, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139 (United States)

    2015-05-07

    For suitably small field emitters, the effects of quantum confinement at the emitter tip may have a significant impact on the emitter performance and total emitted current density (ECD). Since the geometry of a quantum system uniquely determines the magnitude and distribution of its energy levels, a framework for deriving ECD equations from cold field electron emitters of arbitrary geometry and dimensionality is developed. In the interest of obtaining semi-analytical ECD equations, the framework is recast in terms of plane wave solutions to the Schrödinger equation via the use of the Jeffreys-Wentzel-Kramers-Brillouin approximation. To demonstrate the framework's consistency with our previous work and its capabilities in treating emitters with non-planar geometries, ECD equations were derived for the normally unconfined cylindrical nanowire (CNW) and normally confined (NC) CNW emitter geometries. As a function of the emitter radius, the NC CNW emitter ECD profile displayed a strong dependence on the Fermi energy and had an average ECD that exceeded the Fowler-Nordheim equation for typical values of the Fermi energy due to closely spaced, singly degenerate energy levels (excluding electron spin), comparatively large electron supply values, and the lack of a transverse, zero-point energy. Such characteristics suggest that emitters with non-planar geometries may be ideal for emission from both an electron supply and electrostatics perspective.

  9. Biofilm structure and its influence on clogging in drip irrigation emitters distributing reclaimed wastewater

    Institute of Scientific and Technical Information of China (English)

    YAN Dazhuang; BAI Zhihui; Mike Rowan; GU Likun; Ren Shumei; YANG Peiling

    2009-01-01

    Using reclaimed wastewater for crop irrigation is a practical alternative to discharge wastewater treatment plant effluents into surface waters.However,biofouling has been identified as a major contributor to emitter clogging in drip irrigation systems distributing reclaimed wastewater.Little is known about the biofilm structure and its influence on clogging in the drip emitter flow path.This study was first to investigate the microbial characteristics of mature biofilms present in the emitters and the effect of flow path structures on the biofilm microbial communities.The analysis of biofilm matrix structure using a scanning electron microscopy (SEM) revealed that particles in the matrix of the biofilm coupled extracellular polysaccharides (EPS) and formed sediment in the emitter flow path.Analysis of biofilm mass including protein,polysaccharide and phospholipid fatty acids (PLFAs) showed that emitter flow path style influenced biofilm community structure and diversity.The correlations of biofilm biomass and discharge reduction after 360 h irrigation were computed and suggest that PFLAs provide the best correlation coefficient.Comparatively,the emitter with the unsymmetrical dentate structure and shorter flow path (Emitter C) had the best anti-clogging capability.By optimizing the dentate structure,the internal flow pattern within the flow path could be enhanced as an important method to control the biofilm within emitter flow path.This study established electron microscope techniques and biochemical microbial analysis methods that may provide a framework for future emitter biofilm studies.

  10. Transverse emittance growth in staged laser-wakefield acceleration

    Directory of Open Access Journals (Sweden)

    T. Mehrling

    2012-11-01

    Full Text Available We present a study on the emittance evolution of electron bunches, externally injected into laser-driven plasma waves using the three-dimensional particle-in-cell (PIC code OSIRIS. Results show order-of-magnitude transverse emittance growth during the injection process, if the electron bunch is not matched to its intrinsic betatron motion inside the wakefield. This behavior is supported by analytic theory reproducing the simulation data to a percent level. The length over which the full emittance growth develops is found to be less than or comparable to the typical dimension of a single plasma module in current multistage designs. In addition, the analytic theory enables the quantitative prediction of emittance degradation in two consecutive accelerators coupled by free-drift sections, excluding this as a scheme for effective emittance-growth suppression, and thus suggests the necessity of beam-matching sections between acceleration stages with fundamental implications on the overall design of staged laser-wakefield accelerators.

  11. Cellular Taxonomy of the Mouse Striatum as Revealed by Single-Cell RNA-Seq.

    Science.gov (United States)

    Gokce, Ozgun; Stanley, Geoffrey M; Treutlein, Barbara; Neff, Norma F; Camp, J Gray; Malenka, Robert C; Rothwell, Patrick E; Fuccillo, Marc V; Südhof, Thomas C; Quake, Stephen R

    2016-07-26

    The striatum contributes to many cognitive processes and disorders, but its cell types are incompletely characterized. We show that microfluidic and FACS-based single-cell RNA sequencing of mouse striatum provides a well-resolved classification of striatal cell type diversity. Transcriptome analysis revealed ten differentiated, distinct cell types, including neurons, astrocytes, oligodendrocytes, ependymal, immune, and vascular cells, and enabled the discovery of numerous marker genes. Furthermore, we identified two discrete subtypes of medium spiny neurons (MSNs) that have specific markers and that overexpress genes linked to cognitive disorders and addiction. We also describe continuous cellular identities, which increase heterogeneity within discrete cell types. Finally, we identified cell type-specific transcription and splicing factors that shape cellular identities by regulating splicing and expression patterns. Our findings suggest that functional diversity within a complex tissue arises from a small number of discrete cell types, which can exist in a continuous spectrum of functional states.

  12. Cellular Taxonomy of the Mouse Striatum as Revealed by Single-Cell RNA-Seq

    Directory of Open Access Journals (Sweden)

    Ozgun Gokce

    2016-07-01

    Full Text Available The striatum contributes to many cognitive processes and disorders, but its cell types are incompletely characterized. We show that microfluidic and FACS-based single-cell RNA sequencing of mouse striatum provides a well-resolved classification of striatal cell type diversity. Transcriptome analysis revealed ten differentiated, distinct cell types, including neurons, astrocytes, oligodendrocytes, ependymal, immune, and vascular cells, and enabled the discovery of numerous marker genes. Furthermore, we identified two discrete subtypes of medium spiny neurons (MSNs that have specific markers and that overexpress genes linked to cognitive disorders and addiction. We also describe continuous cellular identities, which increase heterogeneity within discrete cell types. Finally, we identified cell type-specific transcription and splicing factors that shape cellular identities by regulating splicing and expression patterns. Our findings suggest that functional diversity within a complex tissue arises from a small number of discrete cell types, which can exist in a continuous spectrum of functional states.

  13. Revealing crystalline domains in a mollusc shell single-crystalline prism

    Science.gov (United States)

    Mastropietro, F.; Godard, P.; Burghammer, M.; Chevallard, C.; Daillant, J.; Duboisset, J.; Allain, M.; Guenoun, P.; Nouet, J.; Chamard, V.

    2017-09-01

    Biomineralization integrates complex processes leading to an extraordinary diversity of calcareous biomineral crystalline architectures, in intriguing contrast with the consistent presence of a sub-micrometric granular structure. Hence, gaining access to the crystalline architecture at the mesoscale, that is, over a few granules, is key to building realistic biomineralization scenarios. Here we provide the nanoscale spatial arrangement of the crystalline structure within the `single-crystalline' prisms of the prismatic layer of a Pinctada margaritifera shell, exploiting three-dimensional X-ray Bragg ptychography microscopy. We reveal the details of the mesocrystalline organization, evidencing a crystalline coherence extending over a few granules. We additionally prove the existence of larger iso-oriented crystalline domains, slightly misoriented with respect to each other, around one unique rotation axis, and whose shapes are correlated with iso-strain domains. The highlighted mesocrystalline properties support recent biomineralization models involving partial fusion of oriented nanoparticle assembly and/or liquid droplet precursors.

  14. Dichotomy of cellular inhibition by small-molecule inhibitors revealed by single-cell analysis

    Science.gov (United States)

    Vogel, Robert M.; Erez, Amir; Altan-Bonnet, Grégoire

    2016-01-01

    Despite progress in drug development, a quantitative and physiological understanding of how small-molecule inhibitors act on cells is lacking. Here, we measure the signalling and proliferative response of individual primary T-lymphocytes to a combination of antigen, cytokine and drug. We uncover two distinct modes of signalling inhibition: digital inhibition (the activated fraction of cells diminishes upon drug treatment, but active cells appear unperturbed), versus analogue inhibition (the activated fraction is unperturbed whereas activation response is diminished). We introduce a computational model of the signalling cascade that accounts for such inhibition dichotomy, and test the model predictions for the phenotypic variability of cellular responses. Finally, we demonstrate that the digital/analogue dichotomy of cellular response as revealed on short (signal transduction) timescales, translates into similar dichotomy on longer (proliferation) timescales. Our single-cell analysis of drug action illustrates the strength of quantitative approaches to translate in vitro pharmacology into functionally relevant cellular settings. PMID:27687249

  15. Hafnia-plugged microcavities for thermal stability of selective emitters

    Science.gov (United States)

    Lee, Heon-Ju; Smyth, Katherine; Bathurst, Stephen; Chou, Jeffrey; Ghebrebrhan, Michael; Joannopoulos, John; Saka, Nannaji; Kim, Sang-Gook

    2013-06-01

    Two-dimensional arrays of micro-cavities effectively control photon motion and selectively emit radiation tailored to the preferred bandgap of photovoltaic (PV) cells, thus enhancing the efficiency of thermophotovoltaic energy conversion. At the high operating temperatures, however, the micro- and nano-patterned structures of the selective emitters quickly lose their integrity--obliterating the tight tolerances required for precise spectral control. Even if oxidation, recrystallization, and grain growth could be avoided with single-crystal tungsten (W) selective emitters with vacuum packaging, surface diffusion, evaporation, and re-condensation are not avoidable in long-term operation at high temperatures. The concept of a planar array of plugged micro-cavities to suppress the curvature-dependent thermal degradation modes is proposed and tested. Based on scale-accelerated failure tests of silicon devices, the lifetime of W selective emitters operating at 1100 K is estimated to be at least 30 yr.

  16. Observation of negative differential transconductance in tunneling emitter bipolar transistors

    Science.gov (United States)

    van Veenhuizen, Marc J.; Locatelli, Nicolas; Moodera, Jagadeesh; Chang, Joonyeon

    2009-08-01

    We report on measurement of negative differential transconductance (NDTC) of iron (Fe)/magnesium-oxide (MgO)/silicon tunneling emitter NPN bipolar transistors. Device simulations reveal that the NDTC is a consequence of an inversion layer at the tunneling-oxide/P-silicon interface for low base voltages. Electrons travel laterally through the inversion layer into the base and give rise to an increase in collector current. The NDTC results from the recombination of those electrons at the interface between emitter and base contact which is dependent on the base voltage. For larger base voltages, the inversion layer disappears marking the onset of normal bipolar transistor behavior.

  17. Counting Vesicular Release Events Reveals Binomial Release Statistics at Single Glutamatergic Synapses.

    Science.gov (United States)

    Malagon, Gerardo; Miki, Takafumi; Llano, Isabel; Neher, Erwin; Marty, Alain

    2016-04-06

    receptors (62%), revealing a larger component of postsynaptic saturation than anticipated. Conversely, we also find that the number of released synaptic vesicles is limited at each active zone. Altogether, our results argue for both presynaptic and postsynaptic contributions to signal saturation at single glutamatergic synapses. Copyright © 2016 the authors 0270-6474/16/364010-16$15.00/0.

  18. Single-Cell Analysis of SMN Reveals Its Broader Role in Neuromuscular Disease

    Directory of Open Access Journals (Sweden)

    Natalia Rodriguez-Muela

    2017-02-01

    Full Text Available The mechanism underlying selective motor neuron (MN death remains an essential question in the MN disease field. The MN disease spinal muscular atrophy (SMA is attributable to reduced levels of the ubiquitous protein SMN. Here, we report that SMN levels are widely variable in MNs within a single genetic background and that this heterogeneity is seen not only in SMA MNs but also in MNs derived from controls and amyotrophic lateral sclerosis (ALS patients. Furthermore, cells with low SMN are more susceptible to cell death. These findings raise the important clinical implication that some SMN-elevating therapeutics might be effective in MN diseases besides SMA. Supporting this, we found that increasing SMN across all MN populations using an Nedd8-activating enzyme inhibitor promotes survival in both SMA and ALS-derived MNs. Altogether, our work demonstrates that examination of human neurons at the single-cell level can reveal alternative strategies to be explored in the treatment of degenerative diseases.

  19. Single-cell genomics reveal metabolic strategies for microbial growth and survival in an oligotrophic aquifer

    Energy Technology Data Exchange (ETDEWEB)

    Wilkins, Michael J.; Kennedy, David W.; Castelle, Cindy; Field, Erin; Stepanauskas, Ramunas; Fredrickson, Jim K.; Konopka, Allan

    2014-02-09

    Bacteria from the genus Pedobacter are a major component of microbial assemblages at Hanford Site and have been shown to significantly change in abundance in response to the subsurface intrusion of Columbia River water. Here we employed single cell genomics techniques to shed light on the physiological niche of these microorganisms. Analysis of four Pedobacter single amplified genomes (SAGs) from Hanford Site sediments revealed a chemoheterotrophic lifestyle, with the potential to exist under both aerobic and microaerophilic conditions via expression of both aa3­-type and cbb3-type cytochrome c oxidases. These SAGs encoded a wide-range of both intra-and extra­-cellular carbohydrate-active enzymes, potentially enabling the degradation of recalcitrant substrates such as xylan and chitin, and the utilization of more labile sugars such as mannose and fucose. Coupled to these enzymes, a diversity of transporters and sugar-binding molecules were involved in the uptake of carbon from the extracellular local environment. The SAGs were enriched in TonB-dependent receptors (TBDRs), which play a key role in uptake of substrates resulting from degradation of recalcitrant carbon. CRISPR-Cas mechanisms for resisting viral infections were identified in all SAGs. These data demonstrate the potential mechanisms utilized for persistence by heterotrophic microorganisms in a carbon-limited aquifer, and hint at potential linkages between observed Pedobacter abundance shifts within the 300 Area subsurface and biogeochemical shifts associated with Columbia River water intrusion.

  20. Mechanical disassembly of single virus particles reveals kinetic intermediates predicted by theory.

    Science.gov (United States)

    Castellanos, Milagros; Pérez, Rebeca; Carrillo, Pablo J P; de Pablo, Pedro J; Mateu, Mauricio G

    2012-06-06

    New experimental approaches are required to detect the elusive transient intermediates predicted by simulations of virus assembly or disassembly. Here, an atomic force microscope (AFM) was used to mechanically induce partial disassembly of single icosahedral T=1 capsids and virions of the minute virus of mice. The kinetic intermediates formed were imaged by AFM. The results revealed that induced disassembly of single minute-virus-of-mice particles is frequently initiated by loss of one of the 20 equivalent capsomers (trimers of capsid protein subunits) leading to a stable, nearly complete particle that does not readily lose further capsomers. With lower frequency, a fairly stable, three-fourths-complete capsid lacking one pentamer of capsomers and a free, stable pentamer were obtained. The intermediates most frequently identified (capsids missing one capsomer, capsids missing one pentamer of capsomers, and free pentamers of capsomers) had been predicted in theoretical studies of reversible capsid assembly based on thermodynamic-kinetic models, molecular dynamics, or oligomerization energies. We conclude that mechanical manipulation and imaging of simple virus particles by AFM can be used to experimentally identify kinetic intermediates predicted by simulations of assembly or disassembly. Copyright © 2012 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  1. Single particle tracking with sterol modulation reveals the cholesterol-mediated diffusion properties of integrin receptors

    Science.gov (United States)

    Arora, Neha; Syed, Aleem; Sander, Suzanne; Smith, Emily A.

    2014-12-01

    A combination of sterol modulation with cyclodextrins plus fluorescence microscopy revealed a biophysical mechanism behind cholesterol’s influence on the diffusion of a ubiquitous class of receptors called integrins. The heterogeneous diffusion of integrins bound to ligand-coated quantum dots was measured using single particle tracking (SPT), and the ensemble changes in integrin diffusion were measured by fluorescence recovery after photobleaching (FRAP). A 25 ± 1% reduction of membrane cholesterol resulted in three significant changes to the diffusion of ligand-bound αPS2CβPS integrins as measured by SPT. There was a 23% increase in ligand-bound mobile integrins; there was a statistically significant increase in the average diffusion coefficient inside zones of confined diffusion, and histograms of confined integrin trajectories showed an increased frequency in the range of 0.1-1 μm2 s-1 and a decreased frequency in the 0.001-0.1 μm2 s-1 range. No statistical change was measured in the duration of confinement nor the size of confined zones. Restoring the cholesterol-depleted cells with exogenous cholesterol or exogenous epicholesterol resulted in similar diffusion properties. Epicholesterol differs from cholesterol in the orientation of a single hydroxyl group. The ability of epicholesterol to substitute for cholesterol suggests a biophysical mechanism for cholesterol’s effect on integrin diffusion. Influences of bilayer thickness, viscosity and organization are discussed as possible explanations for the measured changes in integrin diffusion when the membrane cholesterol concentration is reduced.

  2. Human stem cells from single blastomeres reveal pathways of embryonic or trophoblast fate specification.

    Science.gov (United States)

    Zdravkovic, Tamara; Nazor, Kristopher L; Larocque, Nicholas; Gormley, Matthew; Donne, Matthew; Hunkapillar, Nathan; Giritharan, Gnanaratnam; Bernstein, Harold S; Wei, Grace; Hebrok, Matthias; Zeng, Xianmin; Genbacev, Olga; Mattis, Aras; McMaster, Michael T; Krtolica, Ana; Valbuena, Diana; Simón, Carlos; Laurent, Louise C; Loring, Jeanne F; Fisher, Susan J

    2015-12-01

    Mechanisms of initial cell fate decisions differ among species. To gain insights into lineage allocation in humans, we derived ten human embryonic stem cell lines (designated UCSFB1-10) from single blastomeres of four 8-cell embryos and one 12-cell embryo from a single couple. Compared with numerous conventional lines from blastocysts, they had unique gene expression and DNA methylation patterns that were, in part, indicative of trophoblast competence. At a transcriptional level, UCSFB lines from different embryos were often more closely related than those from the same embryo. As predicted by the transcriptomic data, immunolocalization of EOMES, T brachyury, GDF15 and active β-catenin revealed differential expression among blastomeres of 8- to 10-cell human embryos. The UCSFB lines formed derivatives of the three germ layers and CDX2-positive progeny, from which we derived the first human trophoblast stem cell line. Our data suggest heterogeneity among early-stage blastomeres and that the UCSFB lines have unique properties, indicative of a more immature state than conventional lines.

  3. Pro jected Shell Mo del Description for the Proton Emitters

    Institute of Scientific and Technical Information of China (English)

    卞宝安

    2016-01-01

    Proton radioactivity is an important decay mode for nuclei near the proton drip-line. Studies of this decay mode can reveal valuable information on exotic nuclear structure and provide important information on the stucture of nuclei in extreme conditions. The new experimental data can let us understand the interactions in exotic systems, which motivate further theoretical development. The most recent application of the projected shell model (PSM) for proton emitters is represented. We study the rotational bands of the deformed proton emitter 141Ho by using the PSM. The experimental data are well reproduced. Strongly suppressed γ transition from the low-lying Iπ= 3/2+ state makes this state isomeric. Variations in the dynamical moment of inertia are discussed due to band crossings using the band diagram. The calculated results for proton emitter 151Lu shows it is oblately deformed.

  4. A Papillary Thyroid Microcarcinoma Revealed by a Single Bone Lesion with No Poor Prognostic Factors

    Directory of Open Access Journals (Sweden)

    Yann Godbert

    2013-01-01

    Full Text Available Objectives. Thyroid carcinomas incidence, in particular papillary variants, is increasing. These cancers are generally considered to have excellent prognosis, and papillary microcarcinomas are usually noninvasive. Many prognostic histopathology factors have been described to guide therapeutic decisions. Most patients are treated with total thyroidectomy without radioiodine treatment or partial surgery. Case Summary. A 65-year-old man with no significant medical history presented with pain in the left chest wall that had been present for several months. A computed tomography (CT found a large tissue mass of 4 cm responsible for lysis of the middle arch of the 4th rib on the left. It was a single lesion, highly hypermetabolic on the 18-FDG PET/CT. The histology analysis of the biopsy and surgical specimen favored an adenocarcinoma with immunostaining positive for TTF1 and thyroglobulin (Tg. The total thyroidectomy carried out subsequently revealed a 4 mm papillary microcarcinoma with vesicular architecture of the right lobe, well delimited and distant from the capsule without vascular embolisms. After two radioiodine treatments, the patient is in complete clinical, biological, and radiological remission. Conclusion. This extremely rare case of a singular bone metastasis revealing a papillary thyroid microcarcinoma illustrates the necessity of further research to better characterize the forms of papillary thyroid microcarcinomas with potentially poor prognosis.

  5. Calculation of the detection efficiency in liquid scintillators. II. Single positron emitters; Calculo de la eficiencia de deteccion en liquidos centelleadores. II Nucleidos que se desintegran por emision simple de positrones

    Energy Technology Data Exchange (ETDEWEB)

    Grau Malonda, A.; Garcia Torano, E.

    1982-07-01

    Counting efficiency as a function of the figure of merit for 30 positron emitters has been computed from the positron energy spectrum. Only the efficiency contribution of positrons has been taken into consideration. The contribution of the annihilation photons depending on the volume of the scintillator will be investigated in a near future. Efficiency vs figure of merit is plotted and tabulated. (Author) 19 refs.

  6. Bioluminescence of beetle luciferases with 6'-amino-D-luciferin analogues reveals excited keto-oxyluciferin as the emitter and phenolate/luciferin binding site interactions modulate bioluminescence colors.

    Science.gov (United States)

    Viviani, Vadim R; Neves, Deimison Rodrigues; Amaral, Danilo Trabuco; Prado, Rogilene A; Matsuhashi, Takuto; Hirano, Takashi

    2014-08-19

    Beetle luciferases produce different bioluminescence colors from green to red using the same d-luciferin substrate. Despite many studies of the mechanisms and structural determinants of bioluminescence colors with firefly luciferases, the identity of the emitters and the specific active site interactions responsible for bioluminescence color modulation remain elusive. To address these questions, we analyzed the bioluminescence spectra with 6'-amino-D-luciferin (aminoluciferin) and its 5,5-dimethyl analogue using a set of recombinant beetle luciferases that naturally elicit different colors and different pH sensitivities (pH-sensitive, Amydetes vivianii λmax=538 nm, Macrolampis sp2 λmax=564 nm; pH-insensitive, Phrixotrix hirtus λmax=623 nm, Phrixotrix vivianii λmax=546 nm, and Pyrearinus termitilluminans λmax=534 nm), a luciferase-like enzyme (Tenebrionidae, Zophobas morio λmax=613 nm), and mutants of C311 (S314). The green-yellow-emitting luciferases display red-shifted bioluminescence spectra with aminoluciferin in relation to those with D-luciferin, whereas the red-emitting luciferases displayed blue-shifted spectra. Bioluminescence spectra with 5,5-dimethylaminoluciferin, in which enolization is blocked, were almost identical to those of aminoluciferin. Fluorescence probing using 2-(4-toluidino)naphthalene-6-sulfonate and inference with aminoluciferin confirm that the luciferin binding site of the red-shifted luciferases is more polar than in the case of the green-yellow-emitting luciferases. Altogether, the results show that the keto form of excited oxyluciferin is the emitter in beetle bioluminescence and that bioluminescence colors are essentially modulated by interactions of the 6'-hydroxy group of oxyluciferin and basic moieties under the influence of the microenvironment polarity of the active site: a strong interaction between a base moiety and oxyluciferin phenol in a hydrophobic microenvironment promotes green-yellow emission, whereas a more polar

  7. Electric field distribution of electron emitter surfaces

    Science.gov (United States)

    Tagawa, M.; Takenobu, S.; Ohmae, N.; Umeno, M.

    1987-03-01

    The electric field distribution of a tungsten field emitter surface and a LaB6 thermionic emitter surface has been studied. The computer simulation of electric field distribution on the emitter surface was carried out with a charge simulation method. The electric field distribution of the LaB6 thermionic emitter was experimentally evaluated by the Schottky plot. Two independent equations are necessary for obtaining local electric field and work function; the Fowler-Nordheim equation and the equation of total energy distribution of emitted electron being used to evaluate the electric field distribution of the tungsten field emitter. The experimental results agreed with the computer simulation.

  8. Accelerated Evolution of Ly$\\alpha$ Luminosity Function at $\\textit{z} \\gtrsim 7$ Revealed by the Subaru Ultra-Deep Survey for Ly$\\alpha$ Emitters at $\\textit{z}=7.3$

    CERN Document Server

    Konno, Akira; Ono, Yoshiaki; Shimasaku, Kazuhiro; Shibuya, Takatoshi; Furusawa, Hisanori; Nakajima, Kimihiko; Naito, Yoshiaki; Momose, Rieko; Yuma, Suraphong; Iye, Masanori

    2014-01-01

    We present the ultra-deep Subaru narrowband imaging survey for Lya emitters (LAEs) at $z=7.3$ in SXDS and COSMOS fields with a total integration time of 106 hours. Exploiting our new sharp bandwidth filter, NB101, installed on Suprime-Cam, we have reached $L(Lya)=2.4\\times10^{42} \\ erg \\ s^{-1}$ ($5\\sigma$) for $z=7.3$ LAEs, about 4 times deeper than previous Subaru $z \\gtrsim 7$ studies, which allows us to reliably investigate evolution of Lya luminosity function (LF), for the first time, down to the luminosity limit same as those of Subaru $z=3.1-6.6$ LAE samples. Surprisingly, we only find three and four LAEs in SXDS and COSMOS fields, respectively, while one expects a total of $\\sim 65$ LAEs by our survey in the case of no Lya LF evolution from $z=6.6$ to $7.3$.We identify a decrease of Lya LF from $z=6.6$ to $7.3$ at the $>90\\%$ confidence level from our $z=7.3$ Lya LF.Moreover, the evolution of Lya LF is clearly accelerated at $z>6.6$ beyond the measurement uncertainties including cosmic variance. Becau...

  9. Barium depletion in hollow cathode emitters

    Energy Technology Data Exchange (ETDEWEB)

    Polk, James E., E-mail: james.e.polk@jpl.nasa.gov; Mikellides, Ioannis G.; Katz, Ira [Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California 91109 (United States); Capece, Angela M. [Graduate Aerospace Laboratories, California Institute of Technology, Pasadena, California 91125 (United States)

    2016-01-14

    Dispenser hollow cathodes rely on a consumable supply of Ba released by BaO-CaO-Al{sub 2}O{sub 3} source material in the pores of a tungsten matrix to maintain a low work function surface. The examination of cathode emitters from long duration tests shows deposits of tungsten at the downstream end that appear to block the flow of Ba from the interior. In addition, a numerical model of Ba transport in the cathode plasma indicates that the Ba partial pressure in the insert may exceed the equilibrium vapor pressure of the dominant Ba-producing reaction, and it was postulated previously that this would suppress Ba loss in the upstream part of the emitter. New measurements of the Ba depletion depth from a cathode insert operated for 8200 h reveal that Ba loss is confined to a narrow region near the downstream end, confirming this hypothesis. The Ba transport model was modified to predict the depletion depth with time. A comparison of the calculated and measured depletion depths gives excellent qualitative agreement, and quantitative agreement was obtained assuming an insert temperature 70 °C lower than measured beginning-of-life values.

  10. THEORY OF PROTON EMITTERS

    Energy Technology Data Exchange (ETDEWEB)

    P. TALOU

    2000-08-01

    Modern theoretical methods used to interpret recent experimental data on ground-state proton emission near the proton drip line are reviewed. Most of them are stationary and are aimed to compute proton decay widths {Gamma}{sub p} only. Comparison is made between these approaches before being compared to experimental data. Our time-dependent approach based on the numerical solution of the time-dependent Schroedinger equation (TDSE) for initial quasi-stationary single-proton states is then introduced. It is shown that much deeper insights into the physics of this clean multidimensional quantum tunneling effect can be accessed, and that in addition to {Gamma}{sub p}, other physical quantities could be tested experimentally, offering new stringent tests on nuclear physics models away from the valley of {beta}-stability. Finally, the necessity of using the TDSE approach in more complex, dynamical, problems is demonstrated.

  11. Single-membrane-bounded peroxisome division revealed by isolation of dynamin-based machinery.

    Science.gov (United States)

    Imoto, Yuuta; Kuroiwa, Haruko; Yoshida, Yamato; Ohnuma, Mio; Fujiwara, Takayuki; Yoshida, Masaki; Nishida, Keiji; Yagisawa, Fumi; Hirooka, Shunsuke; Miyagishima, Shin-ya; Misumi, Osami; Kawano, Shigeyuki; Kuroiwa, Tsuneyoshi

    2013-06-01

    Peroxisomes (microbodies) are ubiquitous single-membrane-bounded organelles and fulfill essential roles in the cellular metabolism. They are found in virtually all eukaryotic cells and basically multiply by division. However, the mechanochemical machinery involved in peroxisome division remains elusive. Here, we first identified the peroxisome-dividing (POD) machinery. We isolated the POD machinery from Cyanidioschyzon merolae, a unicellular red alga containing a single peroxisome. Peroxisomal division in C. merolae can be highly synchronized by light/dark cycles and the microtubule-disrupting agent oryzalin. By proteomic analysis based on the complete genome sequence of C. merolae, we identified a dynamin-related protein 3 (DRP3) ortholog, CmDnm1 (Dnm1), that predominantly accumulated with catalase in the dividing-peroxisome fraction. Immunofluorescence microscopy demonstrated that Dnm1 formed a ring at the division site of the peroxisome. The outlines of the isolated dynamin rings were dimly observed by phase-contrast microscopy and clearly stained for Dnm1. Electron microscopy revealed that the POD machinery was formed at the cytoplasmic side of the equator. Immunoelectron microscopy showed that the POD machinery consisted of an outer dynamin-based ring and an inner filamentous ring. Down-regulation of Dnm1 impaired peroxisomal division. Surprisingly, the same Dnm1 serially controlled peroxisomal division after mitochondrial division. Because genetic deficiencies of Dnm1 orthologs in multiperoxisomal organisms inhibited both mitochondrial and peroxisomal proliferation, it is thought that peroxisomal division by contraction of a dynamin-based machinery is universal among eukaryotes. These findings are useful for understanding the fundamental systems in eukaryotic cells.

  12. Extremely low vertical-emittance beam in accelerator-test facility at KEK

    Energy Technology Data Exchange (ETDEWEB)

    Kubo, K.; Akemoto, M.; Anderson, S.; Aoki, T.; Araki, S.; Bane, K.L.F.; Blum, P.; Corlett, J.; Dobashi, K.; Emma, P.; Frisch, J.; Fukuda, M.; Guo, Z.; Hasegawa, K.; Hayano, H.; Higo, T.; Higurashi, A.; Honda, Y.; Iimura, T.; Imai, T.; Jobe, K.; Kamada, S.; Karataev, P.; Kashiwagi, S.; Kim, E.; Kobuki, T.; Kotseroglou, T.; Kurihara, Y.; Kuriki, M.; Kuroda, R.; Kuroda, S.; Lee, T.; Luo, X.; McCormick, D.J.; McKee, B.; Mimashi, T.; Minty, M.; Muto, T.; Naito, Takashi; Naumenko, G.; Nelson, J.; Nguyen, M.N.; Oide, K.; Okugi, T.; Omori, T.; Oshima, T.; Pei, G.; Potylitsyn, A.; Qin, Q.; Raubenheimer, T.; Ross, M.; Sakai, H.; Sakai, I.; Schmidt, F.; Slaton, T.; Smith, H.; Smith, S.; Suzuki, Toshikazu; Takano, M.; Takeda, Seishi; Terunuma, N.; Toge, N.; Turner, J.; Urakawa, J.; Vogel, V.; Woodley, M.; Yocky, J.; Young, A.; Zimmerman, F.; ATF Collaboration

    2002-05-13

    Electron beams with the lowest, normalized transverse emittance recorded so far were produced and confirmed in single-bunch-mode operation of the Accelerator Test Facility at KEK. We established a tuning method of the damping rings which achieves a small vertical dispersion and small x-y orbit coupling. The vertical emittance was less than 1 percent of the horizontal emittance. At the zero-intensity limit, the vertical normalized emittance was less than 2.8 x 10{sup -8} rad m at beam energy 1.3 GeV. At high intensity, strong effects of intrabeam scattering were observed, which had been expected in view of the extremely high particle density due to the small transverse emittance.

  13. Sarcomere dynamics in single myocardial cells as revealed by high-resolution light diffractometry.

    Science.gov (United States)

    Leung, A F

    1983-08-01

    A specially designed diffractometer with a high spatial and temporal resolution recorded the diffraction of a laser beam by single enzymatically isolated myocardial cells. The fine structures within the first-order diffraction were resolved and each structure was interpreted as the diffraction from a group of sarcomeres of nearly equal length. During activation of the cell dynamics of each discrete group of sarcomeres was uniform and independent of the other groups. However, a small nonuniform component in the sarcomere dynamics was observed and attributed to the coupling between the shortening tension and the radial stress resulting from the expansion of the myofibrillar cross-section. The time-course of the diffraction fine structures during contractile activity revealed (1) the period of the contraction-relaxation cycle, (2) the latent period, (3) the shortening and relengthening speeds and (4) the variation in the line width and intensity of the fine structure. Measurements showed that the latent period was dependent on the free Ca2+ of the cell's bathing solution while the initial shortening speed was not. The diffraction line width and intensity of the shortening cell were explained by the grating model.

  14. Single-molecule FRET reveals hidden complexity in a protein energy landscape.

    Science.gov (United States)

    Tsytlonok, Maksym; Ibrahim, Shehu M; Rowling, Pamela J E; Xu, Wenshu; Ruedas-Rama, Maria J; Orte, Angel; Klenerman, David; Itzhaki, Laura S

    2015-01-06

    Here, using single-molecule FRET, we reveal previously hidden conformations of the ankyrin-repeat domain of AnkyrinR, a giant adaptor molecule that anchors integral membrane proteins to the spectrin-actin cytoskeleton through simultaneous binding of multiple partner proteins. We show that the ankyrin repeats switch between high-FRET and low-FRET states, controlled by an unstructured "safety pin" or "staple" from the adjacent domain of AnkyrinR. Opening of the safety pin leads to unravelling of the ankyrin repeat stack, a process that will dramatically affect the relative orientations of AnkyrinR binding partners and, hence, the anchoring of the spectrin-actin cytoskeleton to the membrane. Ankyrin repeats are one of the most ubiquitous molecular recognition platforms in nature, and it is therefore important to understand how their structures are adapted for function. Our results point to a striking mechanism by which the order-disorder transition and, thereby, the activity of repeat proteins can be regulated.

  15. Quantum dot single molecule tracking reveals a wide range of diffusive motions of membrane transport proteins

    Science.gov (United States)

    Crane, Jonathan M.; Haggie, Peter M.; Verkman, A. S.

    2009-02-01

    Single particle tracking (SPT) provides information about the microscopic motions of individual particles in live cells. We applied SPT to study the diffusion of membrane transport proteins in cell plasma membranes in which individual proteins are labeled with quantum dots at engineered extracellular epitopes. Software was created to deduce particle diffusive modes from quantum dot trajectories. SPT of aquaporin (AQP) water channels and cystic fibrosis transmembrane conductance regulator (CFTR) chloride channels revealed several types of diffusion. AQP1 was freely mobile in cell membranes, showing rapid, Brownian-type diffusion. The full-length (M1) isoform of AQP4 also diffused rapidly, though the diffusion of a shorter (M23) isoform of AQP4 was highly restricted due to its supermolecular assembly in raft-like orthogonal arrays. CFTR mobility was also highly restricted, in a spring-like potential, due to its tethering to the actin cytoskeleton through PDZ-domain C-terminus interactions. The biological significance of regulated diffusion of membrane transport proteins is a subject of active investigation.

  16. Single-nanotube tracking reveals the nanoscale organization of the extracellular space in the live brain

    Science.gov (United States)

    Godin, Antoine G.; Varela, Juan A.; Gao, Zhenghong; Danné, Noémie; Dupuis, Julien P.; Lounis, Brahim; Groc, Laurent; Cognet, Laurent

    2017-03-01

    The brain is a dynamic structure with the extracellular space (ECS) taking up almost a quarter of its volume. Signalling molecules, neurotransmitters and nutrients transit via the ECS, which constitutes a key microenvironment for cellular communication and the clearance of toxic metabolites. The spatial organization of the ECS varies during sleep, development and aging and is probably altered in neuropsychiatric and degenerative diseases, as inferred from electron microscopy and macroscopic biophysical investigations. Here we show an approach to directly observe the local ECS structures and rheology in brain tissue using super-resolution imaging. We inject single-walled carbon nanotubes into rat cerebroventricles and follow the near-infrared emission of individual nanotubes as they diffuse inside the ECS for tens of minutes in acute slices. Because of the interplay between the nanotube geometry and the ECS local environment, we can extract information about the dimensions and local viscosity of the ECS. We find a striking diversity of ECS dimensions down to 40 nm, and as well as of local viscosity values. Moreover, by chemically altering the extracellular matrix of the brains of live animals before nanotube injection, we reveal that the rheological properties of the ECS are affected, but these alterations are local and inhomogeneous at the nanoscale.

  17. Single-Molecule Imaging Reveals the Activation Dynamics of Intracellular Protein Smad3 on Cell Membrane

    Science.gov (United States)

    Li, Nan; Yang, Yong; He, Kangmin; Zhang, Fayun; Zhao, Libo; Zhou, Wei; Yuan, Jinghe; Liang, Wei; Fang, Xiaohong

    2016-09-01

    Smad3 is an intracellular protein that plays a key role in propagating transforming growth factor β (TGF-β) signals from cell membrane to nucleus. However whether the transient process of Smad3 activation occurs on cell membrane and how it is regulated remains elusive. Using advanced live-cell single-molecule fluorescence microscopy to image and track fluorescent protein-labeled Smad3, we observed and quantified, for the first time, the dynamics of individual Smad3 molecules docking to and activation on the cell membrane. It was found that Smad3 docked to cell membrane in both unstimulated and stimulated cells, but with different diffusion rates and dissociation kinetics. The change in its membrane docking dynamics can be used to study the activation of Smad3. Our results reveal that Smad3 binds with type I TGF-β receptor (TRI) even in unstimulated cells. Its activation is regulated by TRI phosphorylation but independent of receptor endocytosis. This study offers new information on TGF-β/Smad signaling, as well as a new approach to investigate the activation of intracellular signaling proteins for a better understanding of their functions in signal transduction.

  18. Single-nanotube tracking reveals the nanoscale organization of the extracellular space in the live brain

    Science.gov (United States)

    Godin, Antoine G.; Varela, Juan A.; Gao, Zhenghong; Danné, Noémie; Dupuis, Julien P.; Lounis, Brahim; Groc, Laurent; Cognet, Laurent

    2016-11-01

    The brain is a dynamic structure with the extracellular space (ECS) taking up almost a quarter of its volume. Signalling molecules, neurotransmitters and nutrients transit via the ECS, which constitutes a key microenvironment for cellular communication and the clearance of toxic metabolites. The spatial organization of the ECS varies during sleep, development and aging and is probably altered in neuropsychiatric and degenerative diseases, as inferred from electron microscopy and macroscopic biophysical investigations. Here we show an approach to directly observe the local ECS structures and rheology in brain tissue using super-resolution imaging. We inject single-walled carbon nanotubes into rat cerebroventricles and follow the near-infrared emission of individual nanotubes as they diffuse inside the ECS for tens of minutes in acute slices. Because of the interplay between the nanotube geometry and the ECS local environment, we can extract information about the dimensions and local viscosity of the ECS. We find a striking diversity of ECS dimensions down to 40 nm, and as well as of local viscosity values. Moreover, by chemically altering the extracellular matrix of the brains of live animals before nanotube injection, we reveal that the rheological properties of the ECS are affected, but these alterations are local and inhomogeneous at the nanoscale.

  19. Revealing Assembly of a Pore-Forming Complex Using Single-Cell Kinetic Analysis and Modeling.

    Science.gov (United States)

    Bischofberger, Mirko; Iacovache, Ioan; Boss, Daniel; Naef, Felix; van der Goot, F Gisou; Molina, Nacho

    2016-04-12

    Many biological processes depend on the sequential assembly of protein complexes. However, studying the kinetics of such processes by direct methods is often not feasible. As an important class of such protein complexes, pore-forming toxins start their journey as soluble monomeric proteins, and oligomerize into transmembrane complexes to eventually form pores in the target cell membrane. Here, we monitored pore formation kinetics for the well-characterized bacterial pore-forming toxin aerolysin in single cells in real time to determine the lag times leading to the formation of the first functional pores per cell. Probabilistic modeling of these lag times revealed that one slow and seven equally fast rate-limiting reactions best explain the overall pore formation kinetics. The model predicted that monomer activation is the rate-limiting step for the entire pore formation process. We hypothesized that this could be through release of a propeptide and indeed found that peptide removal abolished these steps. This study illustrates how stochasticity in the kinetics of a complex process can be exploited to identify rate-limiting mechanisms underlying multistep biomolecular assembly pathways.

  20. Mitochondrial specialization revealed by single muscle fiber proteomics: focus on the Krebs cycle.

    Science.gov (United States)

    Schiaffino, S; Reggiani, C; Kostrominova, T Y; Mann, M; Murgia, M

    2015-12-01

    We have developed a highly sensitive mass spectrometry-based proteomic workflow to examine the proteome of single muscle fibers. This study revealed significant differences in the mitochondrial proteome of the four major fiber types present in mouse skeletal muscle. Here, we focus on Krebs cycle enzymes and in particular on the differential distribution of the two mitochondrial isocitrate dehydrogenases, IDH2 and IDH3. Type 1/slow fibers contain high levels of IDH2 and relatively low levels of IDH3, whereas fast 2X and 2B fibers show an opposite expression pattern. The findings suggest that in skeletal muscle, IDH2 functions in the forward direction of the Krebs cycle and that substrate flux along the cycle occurs predominantly via IDH2 in type 1 fibers and via IDH3 in 2X and 2B fibers. IDH2-mediated conversion of isocitrate to α-ketoglutarate leads to the generation of NADPH, which is critical to buffering the H2O2 produced by the respiratory chain. Nicotinamide nucleotide transhydrogenase (NNT), the other major mitochondrial enzyme involved in NADPH generation, is also more abundant in type 1 fibers. We suggest that the continuously active type 1 fibers are endowed with a more efficient H2O2 scavenging capacity to cope with the higher levels of reactive oxygen species production.

  1. Single nucleus genome sequencing reveals high similarity among nuclei of an endomycorrhizal fungus.

    Directory of Open Access Journals (Sweden)

    Kui Lin

    2014-01-01

    Full Text Available Nuclei of arbuscular endomycorrhizal fungi have been described as highly diverse due to their asexual nature and absence of a single cell stage with only one nucleus. This has raised fundamental questions concerning speciation, selection and transmission of the genetic make-up to next generations. Although this concept has become textbook knowledge, it is only based on studying a few loci, including 45S rDNA. To provide a more comprehensive insight into the genetic makeup of arbuscular endomycorrhizal fungi, we applied de novo genome sequencing of individual nuclei of Rhizophagus irregularis. This revealed a surprisingly low level of polymorphism between nuclei. In contrast, within a nucleus, the 45S rDNA repeat unit turned out to be highly diverged. This finding demystifies a long-lasting hypothesis on the complex genetic makeup of arbuscular endomycorrhizal fungi. Subsequent genome assembly resulted in the first draft reference genome sequence of an arbuscular endomycorrhizal fungus. Its length is 141 Mbps, representing over 27,000 protein-coding gene models. We used the genomic sequence to reinvestigate the phylogenetic relationships of Rhizophagus irregularis with other fungal phyla. This unambiguously demonstrated that Glomeromycota are more closely related to Mucoromycotina than to its postulated sister Dikarya.

  2. Single Nucleus Genome Sequencing Reveals High Similarity among Nuclei of an Endomycorrhizal Fungus

    Science.gov (United States)

    Zhang, Zhonghua; Ivanov, Sergey; Saunders, Diane G. O.; Mu, Desheng; Pang, Erli; Cao, Huifen; Cha, Hwangho; Lin, Tao; Zhou, Qian; Shang, Yi; Li, Ying; Sharma, Trupti; van Velzen, Robin; de Ruijter, Norbert; Aanen, Duur K.; Win, Joe; Kamoun, Sophien; Bisseling, Ton; Geurts, René; Huang, Sanwen

    2014-01-01

    Nuclei of arbuscular endomycorrhizal fungi have been described as highly diverse due to their asexual nature and absence of a single cell stage with only one nucleus. This has raised fundamental questions concerning speciation, selection and transmission of the genetic make-up to next generations. Although this concept has become textbook knowledge, it is only based on studying a few loci, including 45S rDNA. To provide a more comprehensive insight into the genetic makeup of arbuscular endomycorrhizal fungi, we applied de novo genome sequencing of individual nuclei of Rhizophagus irregularis. This revealed a surprisingly low level of polymorphism between nuclei. In contrast, within a nucleus, the 45S rDNA repeat unit turned out to be highly diverged. This finding demystifies a long-lasting hypothesis on the complex genetic makeup of arbuscular endomycorrhizal fungi. Subsequent genome assembly resulted in the first draft reference genome sequence of an arbuscular endomycorrhizal fungus. Its length is 141 Mbps, representing over 27,000 protein-coding gene models. We used the genomic sequence to reinvestigate the phylogenetic relationships of Rhizophagus irregularis with other fungal phyla. This unambiguously demonstrated that Glomeromycota are more closely related to Mucoromycotina than to its postulated sister Dikarya. PMID:24415955

  3. Beam emittance measurements at Fermilab

    Energy Technology Data Exchange (ETDEWEB)

    Wendt, Manfred; Eddy, Nathan; Hu, Martin; Scarpine, Victor; Syphers, Mike; Tassotto, Gianni; Thurman-Keup, Randy; Yang, Ming-Jen; Zagel, James; /Fermilab

    2008-01-01

    We give short overview of various beam emittance measurement methods, currently applied at different machine locations for the Run II collider physics program at Fermilab. All these methods are based on beam profile measurements, and we give some examples of the related instrumentation techniques. At the end we introduce a multi-megawatt proton source project, currently under investigation at Fermilab, with respect to the beam instrumentation challenges.

  4. Alpha particle emitters in medicine

    Energy Technology Data Exchange (ETDEWEB)

    Fisher, D.R.

    1989-09-01

    Radiation-induced cancer of bone, liver and lung has been a prominent harmful side-effect of medical applications of alpha emitters. In recent years, however, the potential use of antibodies labeled with alpha emitting radionuclides against cancer has seemed promising because alpha particles are highly effective in cell killing. High dose rates at high LET, effectiveness under hypoxic conditions, and minimal expectancy of repair are additional advantages of alpha emitters over antibodies labeled with beta emitting radionuclides for cancer therapy. Cyclotron-produced astatine-211 ({sup 211}At) and natural bismuth-212 ({sup 212}Bi) have been proposed and are under extensive study in the United States and Europe. Radium-223 ({sup 223}Ra) also has favorable properties as a potential alpha emitting label, including a short-lived daughter chain with four alpha emissions. The radiation dosimetry of internal alpha emitters is complex due to nonuniformly distributed sources, short particle tracks, and high relative specific ionization. The variations in dose at the cellular level may be extreme. Alpha-particle radiation dosimetry, therefore, must involve analysis of statistical energy deposition probabilities for cellular level targets. It must also account fully for nonuniform distributions of sources in tissues, source-target geometries, and particle-track physics. 18 refs., 4 figs.

  5. Coupling of individual quantum emitters to channel plasmons

    CERN Document Server

    Bermúdez-Ureña, Esteban; Geiselmann, Michael; Marty, Renaud; Radko, Ilya P; Holmgaard, Tobias; Alaverdyan, Yury; Moreno, Esteban; García-Vidal, Francisco J; Bozhevolnyi, Sergey I; Quidant, Romain

    2015-01-01

    Efficient light-matter interaction lies at the heart of many emerging technologies that seek on-chip integration of solid-state photonic systems. Plasmonic waveguides, which guide the radiation in the form of strongly confined surface plasmon-polariton modes, represent a promising solution to manipulate single photons in coplanar architectures with unprecedented small footprints. Here we demonstrate coupling of the emission from a single quantum emitter to the channel plasmon polaritons supported by a V-groove plasmonic waveguide. Extensive theoretical simulations enable us to determine the position and orientation of the quantum emitter for optimum coupling. Concomitantly with these predictions, we demonstrate experimentally that 42% of a single nitrogen vacancy centre emission efficiently couples into the supported modes of the V-groove. This work paves the way towards practical realization of efficient and long distance transfer of energy for integrated solid-state quantum systems.

  6. Effects of base resistor on electron emission from a field emitter

    Energy Technology Data Exchange (ETDEWEB)

    Luginsland, J.W.; Valfells, A.; Lau, Y.Y. [Univ. of Michigan, Ann Arbor, MI (United States)

    1996-12-31

    Field emitters have remained an important, high brightness electron source for display and for generation of coherent radiation. The rapid rise in the emitter current with voltage in these emitters leads to serious implications on the emitter stability (thermal, mechanical, and electrical), and an obvious way to improve the emitter stability is to add a series resistor to the emitters. However, the addition of a series resistor would result in a higher operating voltage, loss in efficiency, and much higher cost. In this paper, the authors use a simple model to provide a quantitative analysis of the effects of a base resistor on the voltage-current (V-I) characteristics of a single field emitter. Two features of the present work are noteworthy. First, they present a set of universal curves, from which the effects of a series resistor can immediately be determined once the Fowler-Nordheim coefficients A, B, and the gap spacing D are specified. Thus, these curves are applicable to a large class of field emitters. Second, the calculations take into account the effects of space charge that is present in the gap. The relative importance of the space charge and of the series resistor will become apparent from these curves. Examples will be given.

  7. Group-III Nitride Field Emitters

    Science.gov (United States)

    Bensaoula, Abdelhak; Berishev, Igor

    2008-01-01

    Field-emission devices (cold cathodes) having low electron affinities can be fabricated through lattice-mismatched epitaxial growth of nitrides of elements from group III of the periodic table. Field emission of electrons from solid surfaces is typically utilized in vacuum microelectronic devices, including some display devices. The present field-emission devices and the method of fabricating them were developed to satisfy needs to reduce the cost of fabricating field emitters, make them compatible with established techniques for deposition of and on silicon, and enable monolithic integration of field emitters with silicon-based driving circuitry. In fabricating a device of this type, one deposits a nitride of one or more group-III elements on a substrate of (111) silicon or other suitable material. One example of a suitable deposition process is chemical vapor deposition in a reactor that contains plasma generated by use of electron cyclotron resonance. Under properly chosen growth conditions, the large mismatch between the crystal lattices of the substrate and the nitride causes strains to accumulate in the growing nitride film, such that the associated stresses cause the film to crack. The cracks lie in planes parallel to the direction of growth, so that the growing nitride film becomes divided into microscopic growing single-crystal columns. The outer ends of the fully-grown columns can serve as field-emission tips. By virtue of their chemical compositions and crystalline structures, the columns have low work functions and high electrical conductivities, both of which are desirable for field emission of electrons. From examination of transmission electron micrographs of a prototype device, the average column width was determined to be about 100 nm and the sharpness of the tips was determined to be characterized by a dimension somewhat less than 100 nm. The areal density of the columns was found to about 5 x 10(exp 9)/sq cm . about 4 to 5 orders of magnitude

  8. Single primer amplification reaction methods reveal exotic and indigenous mulberry varieties are similarly diverse

    Indian Academy of Sciences (India)

    Esha Bhattacharya; S B Dandin; Shirish Anand Ranade

    2005-12-01

    Mulberry is the sole food source for mulberry silkworm and a number of indigenous and exotic varieties are used in sericulture. Studies on assessment of genetic diversity have been done amongst a few mulberry varieties using one or at the most two methods. However, no comprehensive study on a large number of varieties has been carried out. In present study, single primer amplification reaction (SPAR) methods have been used for determination of diversity in 27 mulberry varieties (exotic as well as indigenous), using four minisatellite core sequence primers for directed amplification of minisatellite DNA (DAMD), three simple sequence repeat (SSR) motifs as primers for inter simple sequence repeat (ISSR) and 20 arbitrary sequence decamer primers for random amplified polymorphic DNA (RAPD) reactions. The Jaccard coefficients were determined for the DAMD, ISSR and RAPD band data (total of 58, 39 and 235 bands respectively). All three methods revealed wide range of distances supporting a wide range of mulberry genetic diversity. A cumulative analysis of the data generated by three methods resulted in a neighbour-joining (NJ) tree that gave a better reflection of the relatedness and affinities of the varieties to each other. Comparison of the three methods by marker indices and the Mantel test of correlation indicated that though all methods were useful for the assessment of diversity in mulberry, the DAMD method was better. When considered as two groups (10 exotic and 17 indigenous varieties), the mulberry varieties in the exotic group were found to have slightly greater diversity than the indigenous ones. These results support the concept of naturalization of mulberry varieties at locales distant from their origins.

  9. A new method of emittance measurement for electron beams from the Micro-emitter

    Energy Technology Data Exchange (ETDEWEB)

    Ishizuka, Hiroshi [Fukuoka Inst. of Technology (Japan); Nakahara, Yuriko; Kawasaki, Sunao; Musyoki, Stephen; Shimizu, Hiroshi; Watanabe, Akihiko; Shiho, Makoto

    1994-03-01

    Recently a new type of cathode called Micro-emitter is in progress. This cathode is micro fabricated field emitter having the characteristics of very low emittance and high brightness. We can not measure the emittance of the cathode with conventional method like pepper-pot method. The reasons are ; 1. The angle between the electron orbit and the axis is very small. ; and 2. We can not focus the electron beam in the vacuum or on the surface of the material since the current density of the cathode is extremely high. For the emittance measurement for such low emittance and high brightness cathode, we need to expand the beam, and measure the beam cross section without any slits or apertures. We study and propose a new emittance measurement method for the Micro-emitter. (author).

  10. Tunable narrow band source via the strong coupling between optical emitter and nanowire surface plasmons

    CERN Document Server

    Yang, J; Niu, Y P; Qi, Y H; Zhou, F X; Gong, S Q

    2014-01-01

    The spectrum width can be narrowed to a certain degree by decreasing the coupling strength for the two-level emitter coupled to the propagating surface plasmon. But the width can not be narrowed any further because of the loss of the photon out of system by spontaneous emission from the emitter. Here we propose a new scheme to construct a narrow-band source via a one-dimensional waveguide coupling with a three-level emitter. It is shown that the reflective spectrum width can be narrowed avoiding the impact of the loss. This approach opens up the possibility of plasmonic ultranarrow single-photon source.

  11. Impact of Optics on CSR-Related Emittance Growth in Bunch Compressor Chicanes

    CERN Document Server

    Limberg, Torsten

    2005-01-01

    The dependence of emittance growth due to Coherent Synchrotron Radiation (CSR) in bunch compressor chicanes on optics has been noticed and empirically studied in the past. We revisit the subject, suggesting a model to explain slice emittance growth dependence on chicane optics. A simplified model to calculate projected emittance growth when it is mainly caused by transverse slice centroid offsets is presented. It is then used to find optimal compensation of centroid kicks in the single chicanes of a two-stage compression system by adjusting the phase advance of the transport in between and the ration of the compression factors.

  12. Emittance investigation of RF photo-injector

    CERN Document Server

    Yang Mao Rong; Li Zheng; Li Ming; Xu Zhou

    2002-01-01

    A high-power laser beam illuminates a photocathode surface placed on an end wall of an RF cavity. The emitted electrons are accelerated immediately to a relativistic energy by the strong RF find in the cavity. But space charge effect induces beam emittance growth especially near the cathode where the electrons are still nonrelativistic. The author analyzes the factors which lead the transverse emittance growth and method how to resolve this problem. After introducing solenoidal focusing near the photocathode, the beam emittance growth is suppressed dramatically. The beam emittance is given also after compensation and simulation results. The measurements show these results are coincident

  13. Minimum emittance in TBA and MBA lattices

    Science.gov (United States)

    Xu, Gang; Peng, Yue-Mei

    2015-03-01

    For reaching a small emittance in a modern light source, triple bend achromats (TBA), theoretical minimum emittance (TME) and even multiple bend achromats (MBA) have been considered. This paper derived the necessary condition for achieving minimum emittance in TBA and MBA theoretically, where the bending angle of inner dipoles has a factor of 31/3 bigger than that of the outer dipoles. Here, we also calculated the conditions attaining the minimum emittance of TBA related to phase advance in some special cases with a pure mathematics method. These results may give some directions on lattice design.

  14. Single-Cell (Meta-Genomics of a Dimorphic Candidatus Thiomargarita nelsonii Reveals Genomic Plasticity

    Directory of Open Access Journals (Sweden)

    Beverly E. Flood

    2016-05-01

    Full Text Available The genus Thiomargarita includes the world’s largest bacteria. But as uncultured organisms, their physiology, metabolism, and basis for their gigantism are not well understood. Thus a genomics approach, applied to a single Candidatus Thiomargarita nelsonii cell was employed to explore the genetic potential of one of these enigmatic giant bacteria. The Thiomargarita cell was obtained from an assemblage of budding Ca. T. nelsonii attached to a provannid gastropod shell from Hydrate Ridge, a methane seep offshore of Oregon, USA. Here we present a manually curated genome of Bud S10 resulting from a hybrid assembly of long Pacific Biosciences and short Illumina sequencing reads. With respect to inorganic carbon fixation and sulfur oxidation pathways, the Ca. T. nelsonii Hydrate Ridge Bud S10 genome was similar to marine sister taxa within the family Beggiatoaceae. However, the Bud S10 genome contains genes suggestive of the genetic potential for lithotrophic growth on arsenite and perhaps hydrogen. The genome also revealed that Bud S10 likely respires nitrate via two pathways: a complete denitrification pathway and a dissimilatory nitrate reduction to ammonia pathway. Both pathways have been predicted, but not previously fully elucidated, in the genomes of other large, vacuolated, sulfur-oxidizing bacteria.Surprisingly, the genome also had a high number of unusual features for a bacterium to include the largest number of metacaspases and introns ever reported in a bacterium. Also present, are a large number of other mobile genetic elements, such as insertion sequence transposable elements and miniature inverted-repeat transposable elements (MITEs. In some cases, mobile genetic elements disrupted key genes in metabolic pathways. For example, a MITE interrupts hupL, which encodes the large subunit of the hydrogenase in hydrogen oxidation. Moreover, we detected a group I intron in one of the most critical genes in the sulfur oxidation pathway, dsr

  15. Single-Cell (Meta-)Genomics of a Dimorphic Candidatus Thiomargarita nelsonii Reveals Genomic Plasticity

    Science.gov (United States)

    Flood, Beverly E.; Fliss, Palmer; Jones, Daniel S.; Dick, Gregory J.; Jain, Sunit; Kaster, Anne-Kristin; Winkel, Matthias; Mußmann, Marc; Bailey, Jake

    2016-01-01

    The genus Thiomargarita includes the world's largest bacteria. But as uncultured organisms, their physiology, metabolism, and basis for their gigantism are not well understood. Thus, a genomics approach, applied to a single Candidatus Thiomargarita nelsonii cell was employed to explore the genetic potential of one of these enigmatic giant bacteria. The Thiomargarita cell was obtained from an assemblage of budding Ca. T. nelsonii attached to a provannid gastropod shell from Hydrate Ridge, a methane seep offshore of Oregon, USA. Here we present a manually curated genome of Bud S10 resulting from a hybrid assembly of long Pacific Biosciences and short Illumina sequencing reads. With respect to inorganic carbon fixation and sulfur oxidation pathways, the Ca. T. nelsonii Hydrate Ridge Bud S10 genome was similar to marine sister taxa within the family Beggiatoaceae. However, the Bud S10 genome contains genes suggestive of the genetic potential for lithotrophic growth on arsenite and perhaps hydrogen. The genome also revealed that Bud S10 likely respires nitrate via two pathways: a complete denitrification pathway and a dissimilatory nitrate reduction to ammonia pathway. Both pathways have been predicted, but not previously fully elucidated, in the genomes of other large, vacuolated, sulfur-oxidizing bacteria. Surprisingly, the genome also had a high number of unusual features for a bacterium to include the largest number of metacaspases and introns ever reported in a bacterium. Also present, are a large number of other mobile genetic elements, such as insertion sequence (IS) transposable elements and miniature inverted-repeat transposable elements (MITEs). In some cases, mobile genetic elements disrupted key genes in metabolic pathways. For example, a MITE interrupts hupL, which encodes the large subunit of the hydrogenase in hydrogen oxidation. Moreover, we detected a group I intron in one of the most critical genes in the sulfur oxidation pathway, dsrA. The dsrA group

  16. Single-Cell (Meta-)Genomics of a Dimorphic Candidatus Thiomargarita nelsonii Reveals Genomic Plasticity.

    Science.gov (United States)

    Flood, Beverly E; Fliss, Palmer; Jones, Daniel S; Dick, Gregory J; Jain, Sunit; Kaster, Anne-Kristin; Winkel, Matthias; Mußmann, Marc; Bailey, Jake

    2016-01-01

    The genus Thiomargarita includes the world's largest bacteria. But as uncultured organisms, their physiology, metabolism, and basis for their gigantism are not well understood. Thus, a genomics approach, applied to a single Candidatus Thiomargarita nelsonii cell was employed to explore the genetic potential of one of these enigmatic giant bacteria. The Thiomargarita cell was obtained from an assemblage of budding Ca. T. nelsonii attached to a provannid gastropod shell from Hydrate Ridge, a methane seep offshore of Oregon, USA. Here we present a manually curated genome of Bud S10 resulting from a hybrid assembly of long Pacific Biosciences and short Illumina sequencing reads. With respect to inorganic carbon fixation and sulfur oxidation pathways, the Ca. T. nelsonii Hydrate Ridge Bud S10 genome was similar to marine sister taxa within the family Beggiatoaceae. However, the Bud S10 genome contains genes suggestive of the genetic potential for lithotrophic growth on arsenite and perhaps hydrogen. The genome also revealed that Bud S10 likely respires nitrate via two pathways: a complete denitrification pathway and a dissimilatory nitrate reduction to ammonia pathway. Both pathways have been predicted, but not previously fully elucidated, in the genomes of other large, vacuolated, sulfur-oxidizing bacteria. Surprisingly, the genome also had a high number of unusual features for a bacterium to include the largest number of metacaspases and introns ever reported in a bacterium. Also present, are a large number of other mobile genetic elements, such as insertion sequence (IS) transposable elements and miniature inverted-repeat transposable elements (MITEs). In some cases, mobile genetic elements disrupted key genes in metabolic pathways. For example, a MITE interrupts hupL, which encodes the large subunit of the hydrogenase in hydrogen oxidation. Moreover, we detected a group I intron in one of the most critical genes in the sulfur oxidation pathway, dsrA. The dsrA group

  17. Accelerated evolution of the Lyα luminosity function at z ≳ 7 revealed by the Subaru ultra-deep survey for Lyα emitters at z = 7.3

    Energy Technology Data Exchange (ETDEWEB)

    Konno, Akira; Ouchi, Masami; Ono, Yoshiaki; Shibuya, Takatoshi; Naito, Yoshiaki; Momose, Rieko; Yuma, Suraphong [Institute for Cosmic Ray Research, The University of Tokyo, Kashiwa-no-ha, Kashiwa 277-8582 (Japan); Shimasaku, Kazuhiro; Nakajima, Kimihiko [Department of Astronomy, Graduate School of Science, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-0033 (Japan); Furusawa, Hisanori; Iye, Masanori, E-mail: konno@icrr.u-tokyo.ac.jp [National Astronomical Observatory of Japan, 2-21-1 Osawa, Mitaka, Tokyo 181-8588 (Japan)

    2014-12-10

    We present the ultra-deep Subaru narrowband imaging survey for Lyα emitters (LAEs) at z = 7.3 in the Subaru/XMM-Newton Deep Survey (SXDS) and Cosmic Evolution Survey (COSMOS) fields (∼0.5 deg{sup 2}) with a total integration time of 106 hr. Exploiting our new sharp bandwidth filter, NB101, installed on the Suprime-Cam, we have reached L(Lyα) = 2.4 × 10{sup 42} erg s{sup –1} (5σ) for z = 7.3 LAEs, about four times deeper than previous Subaru z ≳ 7 studies, which allows us to reliably investigate the evolution of the Lyα luminosity function (LF) for the first time down to the luminosity limit same as those of Subaru z = 3.1-6.6 LAE samples. Surprisingly, we only find three and four LAEs in the SXDS and COSMOS fields, respectively, while one expects a total of ∼65 LAEs by our survey in the case of no Lyα LF evolution from z = 6.6 to 7.3. We identify a decrease of the Lyα LF from z = 6.6 to 7.3 at the >90% confidence level from our z = 7.3 Lyα LF with the best-fit Schechter parameters of L{sub Lyα}{sup ∗}=2.7{sub −1.2}{sup +8.0}×10{sup 42} erg s{sup −1} and ϕ{sup ∗}=3.7{sub −3.3}{sup +17.6}×10{sup −4} Mpc{sup −3} for a fixed α = –1.5. Moreover, the evolution of the Lyα LF is clearly accelerated at z > 6.6 beyond the measurement uncertainties including cosmic variance. Because no such accelerated evolution of the UV-continuum LF or the cosmic star formation rate (SFR) is found at z ∼ 7, but suggested only at z > 8, this accelerated Lyα LF evolution is explained by physical mechanisms different from a pure SFR decrease but related to the Lyα production and escape in the process of cosmic reionization. Because a simple accelerating increase of intergalactic medium neutral hydrogen absorbing Lyα cannot be reconciled with Thomson scattering of optical depth measurements from WMAP and Planck, our findings may support new physical pictures suggested by recent theoretical studies, such as the existence of HI clumpy clouds within

  18. Voltage controlled optics of a monolayer semiconductor quantum emitter

    Science.gov (United States)

    Chakraborty, Chitraleema; Goodfellow, Kenneth; Kinnischtzke, Laura; Vamivakas, Nick; University of Rochester Team

    2015-03-01

    Two-dimensional atomically thin materials are being actively investigated for next generation optoelectronic devices. Particularly exciting are transition metal dichalcogenides (TMDC) since these materials exhibit a band gap, and support valley specific exciton mediated optical transitions. In this work we report the observation of single photon emission in the TMDC tungsten diselenide. We present magneto-optical spectroscopy results and demonstrate voltage controlled photoluminescence of these localized quantum emitters.

  19. Fast calcium and voltage-sensitive dye imaging in enteric neurones reveal calcium peaks associated with single action potential discharge.

    Science.gov (United States)

    Michel, K; Michaelis, M; Mazzuoli, G; Mueller, K; Vanden Berghe, P; Schemann, M

    2011-12-15

    Slow changes in [Ca(2+)](i) reflect increased neuronal activity. Our study demonstrates that single-trial fast [Ca(2+)](i) imaging (≥200 Hz sampling rate) revealed peaks each of which are associated with single spike discharge recorded by consecutive voltage-sensitive dye (VSD) imaging in enteric neurones and nerve fibres. Fast [Ca(2+)](i) imaging also revealed subthreshold fast excitatory postsynaptic potentials. Nicotine-evoked [Ca(2+)](i) peaks were reduced by -conotoxin and blocked by ruthenium red or tetrodotoxin. Fast [Ca(2+)](i) imaging can be used to directly record single action potentials in enteric neurones. [Ca(2+)](i) peaks required opening of voltage-gated sodium and calcium channels as well as Ca(2+) release from intracellular stores.

  20. Molecular interactions on single-walled carbon nanotubes revealed by high-resolution transmission microscopy

    National Research Council Canada - National Science Library

    Umeyama, Tomokazu; Baek, Jinseok; Sato, Yuta; Suenaga, Kazu; Abou-Chahine, Fawzi; Tkachenko, Nikolai V; Lemmetyinen, Helge; Imahori, Hiroshi

    2015-01-01

    .... Here, we show that the sidewall of a single-walled carbon nanotube (SWNT) represents a unique molecular dimer platform that can be directly visualized using high-resolution transmission electron microscopy...

  1. Mechanism of the superior mechanical strength of nanometer-sized metal single crystals revealed

    KAUST Repository

    Afify, N. D.

    2013-10-01

    Clear understanding of the superior mechanical strength of nanometer-sized metal single crystals is required to derive advanced mechanical components retaining such superiority. Although high quality studies have been reported on nano-crystalline metals, the superiority of small single crystals has neither been fundamentally explained nor quantified to this date. Here we present a molecular dynamics study of aluminum single crystals in the size range from 4.1 nm to 40.5 nm. We show that the ultimate mechanical strength deteriorates exponentially as the single crystal size increases. The small crystals superiority is explained by their ability to continuously form vacancies and to recover them. © 2013 Published by Elsevier B.V.

  2. Compartmental genomics in living cells revealed by single-cell nanobiopsy.

    Science.gov (United States)

    Actis, Paolo; Maalouf, Michelle M; Kim, Hyunsung John; Lohith, Akshar; Vilozny, Boaz; Seger, R Adam; Pourmand, Nader

    2014-01-28

    The ability to study the molecular biology of living single cells in heterogeneous cell populations is essential for next generation analysis of cellular circuitry and function. Here, we developed a single-cell nanobiopsy platform based on scanning ion conductance microscopy (SICM) for continuous sampling of intracellular content from individual cells. The nanobiopsy platform uses electrowetting within a nanopipette to extract cellular material from living cells with minimal disruption of the cellular milieu. We demonstrate the subcellular resolution of the nanobiopsy platform by isolating small subpopulations of mitochondria from single living cells, and quantify mutant mitochondrial genomes in those single cells with high throughput sequencing technology. These findings may provide the foundation for dynamic subcellular genomic analysis.

  3. Diversity of Chemical Mechanisms in Thioredoxin Catalysis Revealed by Single-Molecule Force Spectroscopy

    OpenAIRE

    2009-01-01

    Thioredoxins (Trxs) are oxidoreductase enzymes, present in all organisms, that catalyze the reduction of disulfide bonds in proteins. By applying a calibrated force to a substrate disulfide, the chemical mechanisms of Trx catalysis can be examined in detail at the single-molecule level. Here we use single-molecule force-clamp spectroscopy to explore the chemical evolution of Trx catalysis by probing the chemistry of eight different Trx enzymes. All Trxs show a characteristic Michaelis-Menten ...

  4. Nonlinearly Additive Forces in Multivalent Ligand Binding to a Single Protein Revealed with Force Spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Ratto, T V; Rudd, R E; Langry, K C; Balhorn, R L; McElfresh, M W

    2005-07-15

    We present evidence of multivalent interactions between a single protein molecule and multiple carbohydrates at a pH where the protein can bind four ligands. The evidence is based not only on measurements of the force required to rupture the bonds formed between ConcanavalinA (ConA) and {alpha}-D-mannose, but also on an analysis of the polymer-extension force curves to infer the polymer architecture that binds the protein to the cantilever and the ligands to the substrate. We find that although the rupture forces for multiple carbohydrate connections to a single protein are larger than the rupture force for a single connection, they do not scale additively with increasing number. Specifically, the most common rupture forces are approximately 46, 66, and 85 pN, which we argue corresponds to 1, 2, and 3 ligands being pulled simultaneously from a single protein as corroborated by an analysis of the linkage architecture. As in our previous work polymer tethers allow us to discriminate between specific and non-specific binding. We analyze the binding configuration (i.e. serial versus parallel connections) through fitting the polymer stretching data with modified Worm-Like Chain (WLC) models that predict how the effective stiffness of the tethers is affected by multiple connections. This analysis establishes that the forces we measure are due to single proteins interacting with multiple ligands, the first force spectroscopy study that establishes single-molecule multivalent binding unambiguously.

  5. Spontaneous radiation of a finite-size dipole emitter in hyperbolic media

    CERN Document Server

    Poddubny, Alexander N; Kivshar, Yuri S

    2011-01-01

    We study the radiative decay rate and Purcell effect for a finite-size dipole emitter placed in a homogeneous uniaxial medium. We demonstrate that the radiative rate is strongly enhanced when the signs of the longitudinal and transverse dielectric constants of the medium are opposite, and the isofrequency contour has a hyperbolic shape. We reveal that the Purcell enhancement factor remains finite even in the absence of losses, and it depends on the emitter size.

  6. Design of main linac emittance tuning bumps for the Compact Linear Collider and the International Linear Collider

    Directory of Open Access Journals (Sweden)

    Peder Eliasson

    2008-01-01

    Full Text Available The installation of elements in the main linac of future linear colliders can only be done with a limited precision. The inevitable misalignments lead to unacceptable emittance growth. Beam-based alignment, e.g., one-to-one correction, dispersion free steering, or ballistic alignment, is necessary to reduce the emittance growth. In some cases, this is, however, not sufficient. For further reduction of the emittance growth, so-called emittance tuning bumps have to be used. A general strategy for the design of emittance tuning bumps has been developed and tested. Simulations suggest that the method can be conveniently used to understand the weaknesses of existing emittance tuning bumps and to significantly improve their performance in terms of, e.g., emittance reduction capability and convergence speed. An example of an application is the design of ten orthogonal knobs that, according to simulations, can reduce the normalized emittance growth in the Compact Linear Collider (CLIC main linac from 23.8 to 0.34 nm with convergence within two iterations. Four orthogonal knobs have also been designed for the International Linear Collider (ILC. Simulations show that these knobs converge within a single iteration and reduce normalized emittance growth from 3.8 to 0.05 nm.

  7. Low Emittance X-FEL Development

    CERN Document Server

    Li, K S B; Anghel, A; Bakker, R J; Böge, M; Candel, A E; Dehler, M; Ganter, R; Gough, C; Ingold, G; Leemann, S C; Pedrozzi, M; Raguin, J Y; Rivkin, L; Schlott, V; Streun, A; Wrulich, A F

    2005-01-01

    The Paul Scherrer Institute (PSI) in Switzerland currently develops a Low-Emittance electron-Gun (LEG) based on field-emitter technology [1]. The target is a normalized transverse emittance of 5 10(-8) m rad or less. Such a source is particularly interesting for FELs that target wavelengths below 0.3 nm since it permits a reduction of the required beam-energy and hence, a reduction of the construction- and operational costs of X-ray FELs. That is, for the case that this initial low emittance can be maintained throughout the accelerator. Here we present a concept for a 0.1 nm X-FEL based on LEG, which can be located close to the Swiss Light Source (SLS). Special attention goes to the maintenance of the emittance during the process of acceleration and bunch-compression, in particular in the regimes where either space-charge forces or coherent-synchrotron radiation are of importance.

  8. Batch By Batch Longitudinal Emittance Blowup MD

    CERN Document Server

    Mastoridis, T; Butterworth, A; Jaussi, M; Molendijk, J

    2012-01-01

    The transverse bunch emittance increases significantly at 450 GeV from the time of injection till the ramp due to IBS. By selectively blowing up the longitudinal emittance of the incoming batch at each injection, it should be possible to reduce the transverse emittance growth rates due to IBS. An MD was conducted on April 22nd 2012 to test the feasibility and performance of the batch-by-batch longitudinal emittance blowup. There were three main goals during the MD. First, to test the developed hardware, firmware, and software for the batch-by-batch blowup. Then, to measure the transverse emittance growth rates of blown-up and "witness" batches to quantify any improvement, and finally to test the ALLInjectSequencer class, which deals with the complicated gymnastics of introducing or masking the new batch to various RF loops.

  9. Emittance measurements of the CLIO electron beam

    Science.gov (United States)

    Chaput, R.; Devanz, G.; Joly, P.; Kergosien, B.; Lesrel, J.

    1997-02-01

    We have designed a setup to measure the transverse emittance at the CLIO accelerator exit, based on the "3 gradients" method. The beam transverse size is measured simply by scanning it with a steering coil across a fixed jaw and recording the transmitted current, at various quadrupole strengths. A code then performs a complete calculation of the emittance using the transfer matrix of the quadrupole instead of the usual classical lens approximation. We have studied the influence of various parameters on the emittance: Magnetic field on the e-gun and the peak current. We have also improved a little the emittance by replacing a mismatched pipe between the buncher and accelerating section to avoid wake-field effects; The resulting improvements of the emittance have led to an increase in the FEL emitted power.

  10. Single-cell Hi-C reveals cell-to-cell variability in chromosome structure.

    Science.gov (United States)

    Nagano, Takashi; Lubling, Yaniv; Stevens, Tim J; Schoenfelder, Stefan; Yaffe, Eitan; Dean, Wendy; Laue, Ernest D; Tanay, Amos; Fraser, Peter

    2013-10-03

    Large-scale chromosome structure and spatial nuclear arrangement have been linked to control of gene expression and DNA replication and repair. Genomic techniques based on chromosome conformation capture (3C) assess contacts for millions of loci simultaneously, but do so by averaging chromosome conformations from millions of nuclei. Here we introduce single-cell Hi-C, combined with genome-wide statistical analysis and structural modelling of single-copy X chromosomes, to show that individual chromosomes maintain domain organization at the megabase scale, but show variable cell-to-cell chromosome structures at larger scales. Despite this structural stochasticity, localization of active gene domains to boundaries of chromosome territories is a hallmark of chromosomal conformation. Single-cell Hi-C data bridge current gaps between genomics and microscopy studies of chromosomes, demonstrating how modular organization underlies dynamic chromosome structure, and how this structure is probabilistically linked with genome activity patterns.

  11. Single cell Hi-C reveals cell-to-cell variability in chromosome structure

    Science.gov (United States)

    Schoenfelder, Stefan; Yaffe, Eitan; Dean, Wendy; Laue, Ernest D.; Tanay, Amos; Fraser, Peter

    2013-01-01

    Large-scale chromosome structure and spatial nuclear arrangement have been linked to control of gene expression and DNA replication and repair. Genomic techniques based on chromosome conformation capture assess contacts for millions of loci simultaneously, but do so by averaging chromosome conformations from millions of nuclei. Here we introduce single cell Hi-C, combined with genome-wide statistical analysis and structural modeling of single copy X chromosomes, to show that individual chromosomes maintain domain organisation at the megabase scale, but show variable cell-to-cell chromosome territory structures at larger scales. Despite this structural stochasticity, localisation of active gene domains to boundaries of territories is a hallmark of chromosomal conformation. Single cell Hi-C data bridge current gaps between genomics and microscopy studies of chromosomes, demonstrating how modular organisation underlies dynamic chromosome structure, and how this structure is probabilistically linked with genome activity patterns. PMID:24067610

  12. Diversity of Chemical Mechanisms in Thioredoxin Catalysis Revealed by Single-Molecule Force Spectroscopy

    Science.gov (United States)

    Perez-Jimenez, Raul; Li, Jingyuan; Kosuri, Pallav; Sanchez-Romero, Inmaculada; Wiita, Arun P.; Rodriguez-Larrea, David; Chueca, Ana; Holmgren, Arne; Miranda-Vizuete, Antonio; Becker, Katja; Cho, Seung-Hyun; Beckwith, Jon; Gelhaye, Eric; Jacquot, Jean P.; Gaucher, Eric; Sanchez-Ruiz, Jose M.; Berne, Bruce J.; Fernandez, Julio M.

    2009-01-01

    Thioredoxins are oxido-reductase enzymes present in all organisms, catalyzing the reduction of disulfide bonds in proteins. By applying a calibrated force to a substrate disulfide, the chemical mechanisms of Trx catalysis can be examined in detail at the single molecule level. Here we use single molecule force-clamp spectroscopy to explore the chemical evolution of Trx catalysis by probing the chemistry of eight different thioredoxin enzymes. While all Trxs show a characteristic Michaelis-Menten mechanism detected when the disulfide bond is stretched at low forces, two different chemical behaviors distinguish bacterial from eukaryotic-origin Trxs at high forces. Eukaryotic-origin Trxs reduce disulfide bonds through a single-electron transfer reaction (SET) whereas bacterial-origin Trxs exhibit both nucleophilic substitution (SN2) and SET reactions. A computational analysis of Trx structures identifies the evolution of the binding groove as an important factor controlling the chemistry of Trx catalysis. PMID:19597482

  13. Single cell sequencing reveals heterogeneity within ovarian cancer epithelium and cancer associated stromal cells.

    Science.gov (United States)

    Winterhoff, Boris J; Maile, Makayla; Mitra, Amit Kumar; Sebe, Attila; Bazzaro, Martina; Geller, Melissa A; Abrahante, Juan E; Klein, Molly; Hellweg, Raffaele; Mullany, Sally A; Beckman, Kenneth; Daniel, Jerry; Starr, Timothy K

    2017-03-01

    The purpose of this study was to determine the level of heterogeneity in high grade serous ovarian cancer (HGSOC) by analyzing RNA expression in single epithelial and cancer associated stromal cells. In addition, we explored the possibility of identifying subgroups based on pathway activation and pre-defined signatures from cancer stem cells and chemo-resistant cells. A fresh, HGSOC tumor specimen derived from ovary was enzymatically digested and depleted of immune infiltrating cells. RNA sequencing was performed on 92 single cells and 66 of these single cell datasets passed quality control checks. Sequences were analyzed using multiple bioinformatics tools, including clustering, principle components analysis, and geneset enrichment analysis to identify subgroups and activated pathways. Immunohistochemistry for ovarian cancer, stem cell and stromal markers was performed on adjacent tumor sections. Analysis of the gene expression patterns identified two major subsets of cells characterized by epithelial and stromal gene expression patterns. The epithelial group was characterized by proliferative genes including genes associated with oxidative phosphorylation and MYC activity, while the stromal group was characterized by increased expression of extracellular matrix (ECM) genes and genes associated with epithelial-to-mesenchymal transition (EMT). Neither group expressed a signature correlating with published chemo-resistant gene signatures, but many cells, predominantly in the stromal subgroup, expressed markers associated with cancer stem cells. Single cell sequencing provides a means of identifying subpopulations of cancer cells within a single patient. Single cell sequence analysis may prove to be critical for understanding the etiology, progression and drug resistance in ovarian cancer. Copyright © 2017 Elsevier Inc. All rights reserved.

  14. Nonequilibrium Chemical Effects in Single-Molecule SERS Revealed by Ab Initio Molecular Dynamics Simulations

    Energy Technology Data Exchange (ETDEWEB)

    Fischer, Sean A.; Apra, Edoardo; Govind, Niranjan; Hess, Wayne P.; El-Khoury, Patrick Z.

    2017-02-03

    Recent developments in nanophotonics have paved the way for achieving significant advances in the realm of single molecule chemical detection, imaging, and dynamics. In particular, surface-enhanced Raman scattering (SERS) is a powerful analytical technique that is now routinely used to identify the chemical identity of single molecules. Understanding how nanoscale physical and chemical processes affect single molecule SERS spectra and selection rules is a challenging task, and is still actively debated. Herein, we explore underappreciated chemical phenomena in ultrasensitive SERS. We observe a fluctuating excited electronic state manifold, governed by the conformational dynamics of a molecule (4,4’-dimercaptostilbene, DMS) interacting with a metallic cluster (Ag20). This affects our simulated single molecule SERS spectra; the time trajectories of a molecule interacting with its unique local environment dictates the relative intensities of the observable Raman-active vibrational states. Ab initio molecular dynamics of a model Ag20-DMS system are used to illustrate both concepts in light of recent experimental results.

  15. Single nucleus genome sequencing reveals high similarity among nuclei of an endomycorrhizal fungus

    NARCIS (Netherlands)

    Lin, K.; Limpens, E.H.M.; Zhang, Z.; Ivanov, S.; Saunders, D.G.O.; Mu, D.; Pang, E.; Cao, H.; Cha, H.; Lin, T.; Zhou, Q.; Shang, Y.; Li, Y.; Sharma, T.C.; Velzen, van R.; Ruijter, de N.C.A.; Aanen, D.K.; Win, J.; Kamoun, S.; Bisseling, T.; Geurts, R.; Huang, S.W.

    2014-01-01

    Nuclei of arbuscular endomycorrhizal fungi have been described as highly diverse due to their asexual nature and absence of a single cell stage with only one nucleus. This has raised fundamental questions concerning speciation, selection and transmission of the genetic make-up to next generations. A

  16. Deep amplicon sequencing reveals mixed phytoplasma infection within single grapevine plants

    DEFF Research Database (Denmark)

    Nicolaisen, Mogens; Contaldo, Nicoletta; Makarova, Olga

    2011-01-01

    The diversity of phytoplasmas within single plants has not yet been fully investigated. In this project, deep amplicon sequencing was used to generate 50,926 phytoplasma sequences from 11 phytoplasma-infected grapevine samples from a PCR amplicon in the 5' end of the 16S region. After clustering ...

  17. Single base-resolution methylome of the silkworm reveals a sparse epigenomic map

    DEFF Research Database (Denmark)

    Xiang, Hui; Zhu, Jingde; Chen, Quan;

    2010-01-01

    Epigenetic regulation in insects may have effects on diverse biological processes. Here we survey the methylome of a model insect, the silkworm Bombyx mori, at single-base resolution using Illumina high-throughput bisulfite sequencing (MethylC-Seq). We conservatively estimate that 0.11% of genomic...

  18. High-Speed AFM Reveals the Dynamics of Single Biomolecules at the Nanometer Scale

    NARCIS (Netherlands)

    Katan, A.J.; Dekker, C.

    2011-01-01

    Atomic force microscopy allows visualization of biomolecules with nanometer resolution under physiological conditions. Recent advances have improved the time resolution of the technique from minutes to tens of milliseconds, meaning that it is now possible to watch single biomolecules in action in re

  19. High-Speed AFM Reveals the Dynamics of Single Biomolecules at the Nanometer Scale

    NARCIS (Netherlands)

    Katan, A.J.; Dekker, C.

    2011-01-01

    Atomic force microscopy allows visualization of biomolecules with nanometer resolution under physiological conditions. Recent advances have improved the time resolution of the technique from minutes to tens of milliseconds, meaning that it is now possible to watch single biomolecules in action in re

  20. Deep amplicon sequencing reveals mixed phytoplasma infection within single grapevine plants

    DEFF Research Database (Denmark)

    Nicolaisen, Mogens; Contaldo, Nicoletta; Makarova, Olga

    2011-01-01

    The diversity of phytoplasmas within single plants has not yet been fully investigated. In this project, deep amplicon sequencing was used to generate 50,926 phytoplasma sequences from 11 phytoplasma-infected grapevine samples from a PCR amplicon in the 5' end of the 16S region. After clustering ...

  1. High-Precision Resonant Cavity Beam Position, Emittance And Third-Moment Monitors

    Energy Technology Data Exchange (ETDEWEB)

    Barov, N.; Kim, J.S.; Weidemann, A.W.; /FARTECH, San Diego; Miller, R.H.; Nantista, C.D.; /SLAC

    2006-03-14

    Linear colliders and FEL facilities need fast, nondestructive beam position and profile monitors to facilitate machine tune-up, and for use with feedback control. FAR-TECH, Inc., in collaboration with SLAC, is developing a resonant cavity diagnostic to simultaneously measure the dipole, quadrupole and sextupole moments of the beam distribution. Measurements of dipole and quadrupole moments at multiple locations yield information about beam orbit and emittance. The sextupole moment can reveal information about beam asymmetry which is useful in diagnosing beam tail deflections caused by short-range dipole wakefields. In addition to the resonance enhancement of a single-cell cavity, use of a multi-cell standing-wave structure further enhances signal strength and improves the resolution of the device. An estimated resolution is better than 1 {micro}m in rms beam size and better than 1 nm in beam position.

  2. Low Emittance Electron Beam Studies

    Energy Technology Data Exchange (ETDEWEB)

    Tikhoplav, Rodion [Univ. of Rochester, NY (United States)

    2006-01-01

    We have studied the properties of a low emittance electron beam produced by laser pulses incident onto an rf gun photocathode. The experiments were carried out at the A0 photoinjector at Fermilab. Such beam studies are necessary for fixing the design of new Linear Colliders as well as for the development of Free Electron Lasers. An overview of the A0 photoinjector is given in Chapter 1. In Chapter 2 we describe the A0 photoinjector laser system. A stable laser system is imperative for reliable photoinjector operation. After the recent upgrade, we have been able to reach a new level of stability in the pulse-to-pulse fluctuations of the pulse amplitude, and of the temporal and transverse profiles. In Chapter 3 we present a study of transverse emittance versus the shape of the photo-cathode drive-laser pulse. For that purpose a special temporal profile laser shaping device called a pulse-stacker was developed. In Chapter 4 we discuss longitudinal beam dynamics studies using a two macro-particle bunch; this technique is helpful in analyzing pulse compression in the magnetic chicane, as well as velocity bunching effects in the rf-gun and the 9-cell accelerating cavity. In Chapter 5 we introduce a proposal for laser acceleration of electrons. We have developed a laser functioning on the TEM*01 mode, a mode with a longitudinal electric field component which is suitable for such a process. Using this technique at energies above 40 MeV, one would be able to observe laser-based acceleration.

  3. Nanoseconds field emitted current pulses from ZrC needles and field emitter arrays

    CERN Document Server

    Ganter, R; Betemps, R; Dehler, M; Gerber, T; Gobrecht, J; Gough, C; Johnson, M; Kirk, E; Knopp, G; Le Pimpec, F; Li, K; Paraliev, M; Pedrozzi, M; Rivkin, L; Schulz, L; Sehr, H; Wrulich, A F

    2006-01-01

    The properties of the electron source define the ultimate limit of the beam quality in linear accelerators like Free Electron Lasers (FEL). The goal is to develop an electron gun delivering beam emittance lower than current state of the art. Such a gun should reduce the cost and size of an X-ray Free Electron Laser (XFEL). In this paper we present two concepts of field emitter cathodes which could potentially produce low emittance beam. The first challenging parameter for such cathode is to emit peak current as high as 5 A. This is the minimum current requirement for the XFEL concept from Paul Scherrer Institut.1 Maximum current of 0.12 A and 0.58 A have been reached respectively with field emitter arrays (FEA) and single needle cathodes. Laser assisted field emission gave encouraging results to reach even higher peak current and to pre-bunch the beam.

  4. Demonstration of Cathode Emittance Dominated High Bunch Charge Beams in a DC gun-based Photoinjector

    CERN Document Server

    Gulliford, Colwyn; Bazarov, Ivan; Dunham, Bruce; Cultrera, Luca

    2015-01-01

    We present the results of transverse emittance and longitudinal current profile measurements of high bunch charge (greater than or equal to 100 pC) beams produced in the DC gun-based Cornell Energy Recovery Linac Photoinjector. In particular, we show that the cathode thermal and core beam emittances dominate the final 95% and core emittance measured at 9-9.5 MeV. Additionally, we demonstrate excellent agreement between optimized 3D space charge simulations and measurement, and show that the quality of the transverse laser distribution limits the optimal simulated and measured emittances. These results, previously thought achievable only with RF guns, demonstrate that DC gun based photoinjectors are capable of delivering beams with sufficient single bunch charge and beam quality suitable for many current and next generation accelerator projects such as Energy Recovery Linacs (ERLs) and Free Electron Lasers (FELs).

  5. Measurement of a small vertical emittance with a laser wire beam profile monitor

    Directory of Open Access Journals (Sweden)

    Hiroshi Sakai

    2002-12-01

    Full Text Available We describe in this paper a measurement of vertical emittance in the Accelerator Test Facility (ATF damping ring at KEK with a laser wire beam profile monitor. This monitor is based on the Compton scattering process of electrons with a laser light target which is produced by injecting a cw laser beam into a Fabry-Perot optical cavity. We installed the monitor at a straight section of the damping ring and measured the vertical emittance with three different ring conditions. In all cases, the ATF ring was operated at 1.28 GeV in a single bunch mode. When the ring was tuned for ultralow emittance, the vertical emittance of ε_{y}=(1.18±0.08×10^{-11}   mrad was achieved. This shows that the ATF damping ring has realized its target value also vertically.

  6. Emitter and absorber assembly for multiple self-dual operation and directional transparency

    CERN Document Server

    Kalozoumis, P A; Kodaxis, G; Diakonos, F K; Schmelcher, P

    2016-01-01

    A recursive scheme for the design of scatterers acting simultaneously as emitters and absorbers, such as lasers and coherent perfect absorbers in optics, at multiple prescribed frequencies is proposed. The approach is based on the assembly of non-Hermitian emitter and absorber units into self-dual emitter-absorber trimers at different composition levels, exploiting the simple structure of the corresponding transfer matrices. In particular, lifting the restriction to parity-time-symmetric setups enables the realization of emitter and absorber action at distinct frequencies and provides flexibility in the choice of realistic parameters. We further show how the same assembled scatterers can be rearranged to produce unidirectional and bidirectional transparency at the selected frequencies. With the design procedure being generically applicable to wave scattering in single-channel settings, we demonstrate it with concrete examples of photonic multilayer setups.

  7. Environmental genomics reveals a single species ecosystem deep within the Earth

    Energy Technology Data Exchange (ETDEWEB)

    Chivian, Dylan; Brodie, Eoin L.; Alm, Eric J.; Culley, David E.; Dehal, Paramvir S.; DeSantis, Todd Z.; Gihring, Thomas M.; Lapidus, Alla; Lin, Li-Hung; Lowry, Stephen R.; Moser, Duane P.; Richardson, Paul; Southam, Gordon; Wanger, Greg; Pratt, Lisa M.; Andersen, Gary L.; Hazen, Terry C.; Brockman, Fred J.; Arkin, Adam P.; Onstott, Tullis C.

    2008-09-17

    DNA from low biodiversity fracture water collected at 2.8 km depth in a South African gold mine was sequenced and assembled into a single, complete genome. This bacterium, Candidatus Desulforudis audaxviator, comprises>99.9percent of the microorganisms inhabiting the fluid phase of this particular fracture. Its genome indicates a motile, sporulating, sulfate reducing, chemoautotrophic thermophile that can fix its own nitrogen and carbon using machinery shared with archaea. Candidatus Desulforudis audaxviator is capable of an independent lifestyle well suited to long-term isolation from the photosphere deep within Earth?s crust, and offers the first example of a natural ecosystem that appears to have its biological component entirely encoded within a single genome.

  8. HIGH-SPEED SINGLE QUANTUM DOT IMAGING OF IN LIVE CELLS REVEAL HOP DIFFUSION

    DEFF Research Database (Denmark)

    Lagerholm, B. Christoffer; Clausen, Mathias P.

    2011-01-01

    Ultra high-speed single particle tracking (image frame rates 40-50 kHz) experiments with 40 nm gold particles has indicated that lipids and proteins in the plasma membrane undergo hop-diffusion between nanometer sized compartments (Fujiwara et al. (2002) J Cell Biol. 157:1071-81). These findings...... have yet to be independently confirmed. In this work, we show that high-speed single particle tracking with quantum dots (QDs) and using a standard wide-field fluorescence microscope and an EMCCD is possible at image acquisition rates of up to ~2000 Hz. The spatial precision in these experiments is ~40...... nm (as determined from the standard deviation of repeated position measurements of an immobile QD on a cell). Using this system, we show that membrane proteins and lipids, which have been exogenously labeled with functionalized QDs, show examples of three types of motion in the plasma membrane...

  9. Revealing low-dose radiation damage using single-crystal spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Owen, Robin L., E-mail: robin.owen@diamond.ac.uk [Diamond Light Source Ltd, Diamond House, Harwell Science and Innovation Campus, Didcot, OX11 0DE (United Kingdom); Yorke, Briony A.; Gowdy, James A.; Pearson, Arwen R. [University of Leeds, Leeds (United Kingdom)

    2011-05-01

    Data on the rapid reduction of haem proteins in the X-ray beam at synchrotron sources are presented. The use of single-crystal spectroscopy to detect these changes and their implication for diffraction data collection from oxidized species is also discussed. The structural information and functional insight obtained from X-ray crystallography can be enhanced by the use of complementary spectroscopies. Here the information that can be obtained from spectroscopic methods commonly used in conjunction with X-ray crystallography and best-practice single-crystal UV-Vis absorption data collection are briefly reviewed. Using data collected with the in situ system at the Swiss Light Source, the time and dose scales of low-dose X-ray-induced radiation damage and solvated electron generation in metalloproteins at 100 K are investigated. The effect of dose rate on these scales is also discussed.

  10. Multilocus sequence analysis of Fusarium pseudograminearum reveals a single phylogenetic species.

    Science.gov (United States)

    Scott, Jason B; Chakraborty, Sukumar

    2006-12-01

    Fusarium pseudograminearum causes crown rot of wheat in Australia and most other wheat growing regions, but its evolutionary history is largely unknown. We demonstrate for the first time that F. pseudograminearum is a single phylogenetic species without consistent lineage development across genes. Isolates of F. pseudograminearum, F. graminearum sensu lato, and F. cerealis, were collected from four countries and four single copy, nuclear genes were partially sequenced, aligned with previously published sequences of these and related species, and analysed by maximum parsimony and Bayesian inference. Evolutionary divergence varied between genes, with high phylogenetic incongruence occurring between the gene genealogies. The absence of geographic differentiation between isolates indicates that the introduction of new fungal strains to a region has the potential to introduce new pathogenic and toxigenic genes into the native population through sexual recombination.

  11. Exome Sequencing Reveals Cubilin Mutation as a Single-Gene Cause of Proteinuria

    Science.gov (United States)

    Ovunc, Bugsu; Otto, Edgar A.; Vega-Warner, Virginia; Saisawat, Pawaree; Ashraf, Shazia; Ramaswami, Gokul; Fathy, Hanan M.; Schoeb, Dominik; Chernin, Gil; Lyons, Robert H.; Yilmaz, Engin

    2011-01-01

    In two siblings of consanguineous parents with intermittent nephrotic-range proteinuria, we identified a homozygous deleterious frameshift mutation in the gene CUBN, which encodes cubulin, using exome capture and massively parallel re-sequencing. The mutation segregated with affected members of this family and was absent from 92 healthy individuals, thereby identifying a recessive mutation in CUBN as the single-gene cause of proteinuria in this sibship. Cubulin mutations cause a hereditary form of megaloblastic anemia secondary to vitamin B12 deficiency, and proteinuria occurs in 50% of cases since cubilin is coreceptor for both the intestinal vitamin B12-intrinsic factor complex and the tubular reabsorption of protein in the proximal tubule. In summary, we report successful use of exome capture and massively parallel re-sequencing to identify a rare, single-gene cause of nephropathy. PMID:21903995

  12. Exome sequencing reveals cubilin mutation as a single-gene cause of proteinuria.

    Science.gov (United States)

    Ovunc, Bugsu; Otto, Edgar A; Vega-Warner, Virginia; Saisawat, Pawaree; Ashraf, Shazia; Ramaswami, Gokul; Fathy, Hanan M; Schoeb, Dominik; Chernin, Gil; Lyons, Robert H; Yilmaz, Engin; Hildebrandt, Friedhelm

    2011-10-01

    In two siblings of consanguineous parents with intermittent nephrotic-range proteinuria, we identified a homozygous deleterious frameshift mutation in the gene CUBN, which encodes cubulin, using exome capture and massively parallel re-sequencing. The mutation segregated with affected members of this family and was absent from 92 healthy individuals, thereby identifying a recessive mutation in CUBN as the single-gene cause of proteinuria in this sibship. Cubulin mutations cause a hereditary form of megaloblastic anemia secondary to vitamin B(12) deficiency, and proteinuria occurs in 50% of cases since cubilin is coreceptor for both the intestinal vitamin B(12)-intrinsic factor complex and the tubular reabsorption of protein in the proximal tubule. In summary, we report successful use of exome capture and massively parallel re-sequencing to identify a rare, single-gene cause of nephropathy.

  13. Div-Seq: Single-nucleus RNA-Seq reveals dynamics of rare adult newborn neurons.

    Science.gov (United States)

    Habib, Naomi; Li, Yinqing; Heidenreich, Matthias; Swiech, Lukasz; Avraham-Davidi, Inbal; Trombetta, John J; Hession, Cynthia; Zhang, Feng; Regev, Aviv

    2016-08-26

    Single-cell RNA sequencing (RNA-Seq) provides rich information about cell types and states. However, it is difficult to capture rare dynamic processes, such as adult neurogenesis, because isolation of rare neurons from adult tissue is challenging and markers for each phase are limited. Here, we develop Div-Seq, which combines scalable single-nucleus RNA-Seq (sNuc-Seq) with pulse labeling of proliferating cells by 5-ethynyl-2'-deoxyuridine (EdU) to profile individual dividing cells. sNuc-Seq and Div-Seq can sensitively identify closely related hippocampal cell types and track transcriptional dynamics of newborn neurons within the adult hippocampal neurogenic niche, respectively. We also apply Div-Seq to identify and profile rare newborn neurons in the adult spinal cord, a noncanonical neurogenic region. sNuc-Seq and Div-Seq open the way for unbiased analysis of diverse complex tissues.

  14. Exome Sequencing Reveals Cubilin Mutation as a Single-Gene Cause of Proteinuria

    OpenAIRE

    Ovunc, Bugsu; Otto, Edgar A.; Vega-Warner, Virginia; Saisawat, Pawaree; Ashraf, Shazia; Ramaswami, Gokul; Fathy, Hanan M.; Schoeb, Dominik; Chernin, Gil; Lyons, Robert H.; Engin YILMAZ; Hildebrandt, Friedhelm

    2011-01-01

    In two siblings of consanguineous parents with intermittent nephrotic-range proteinuria, we identified a homozygous deleterious frameshift mutation in the gene CUBN, which encodes cubulin, using exome capture and massively parallel re-sequencing. The mutation segregated with affected members of this family and was absent from 92 healthy individuals, thereby identifying a recessive mutation in CUBN as the single-gene cause of proteinuria in this sibship. Cubulin mutations cause a hereditary fo...

  15. Crack tip dislocations revealed by electron tomography in silicon single crystal

    Energy Technology Data Exchange (ETDEWEB)

    Tanaka, Masaki [Department of Materials Science and Engineering, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395 (Japan)], E-mail: masaki@zaiko.kyushu-u.ac.jp; Higashida, Kenji [Department of Materials Science and Engineering, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395 (Japan); Kaneko, Kenji [Department of Materials Science and Engineering, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395 (Japan); JST-CREST, 744 Motooka, Nishi-ku, Fukuoka 819-0395 (Japan); Hata, Satoshi; Mitsuhara, Masatoshi [Department of Engineering Sciences for Electronics and Materials, Kyushu University, 6-1 Kasuga koen, Kasuga, Fukuoka 816-8580 (Japan)

    2008-10-15

    Crack tip dislocations in silicon single crystals have been observed by a combination of annular dark-field scanning transmission electron microscopy and computed tomography. A series of images was acquired by maintaining the diffraction vector parallel to that of crack propagation to achieve sharp images of the dislocations. The observed dislocations were reconstructed by a filtered back-projection, and exhibited three-dimensional configurations of overlaid dislocations around the crack tip.

  16. Environmental genomics reveals a single-species ecosystem deep within earth

    Energy Technology Data Exchange (ETDEWEB)

    Chivian, Dylan; Brodie, Eoin L.; Alm, Eric; Culley, David E.; Dehal, Paramvir S.; DeSantis, Todd; Gihring, Thomas M.; Lapidus, Alla; Lin, Li-Hung; Lowry, Stephen R.; Moser, Duane P.; Richardson, Paul; Southam, G.; Wanger, G.; Pratt, L. M.; Andersen, Gary; Hazen, Terry C.; Brockman, Fred J.; Arkin, Adam P.; Onstott, T. C.

    2008-10-10

    DNA from low biodiversity, 3 to 40 myr old, fracture water collected at 2.8 km depth in a South African gold mine was sequenced and assembled into a single, complete genome. This uncultured Gram-positive bacterium, Candidatus Desulforudis audaxviator, is prevalent at depths > 1.5 km in the Witwatersrand Basin and its near-clonal population comprises > 99.9% of the microorganisms inhabiting the fluid phase of this particular fracture. Only 0.0014% of the 2.35 Mb exhibit polymorphism, which is almost 60 fold less than the 0.08% rate found for the unusually homogeneous Leptospirillum group II population present in a single biofilm sample from the Iron Mt. acid mine drainage community. Its genome indicates a motile, sporulating, sulfate (SO42-) reducing, chemoautotrophic thermophile that is capable of fixing its own nitrogen and carbon using machinery shared with archaea. Candidatus Desulforudis audaxviator appears capable of an independent lifestyle well suited to long-term isolation from the photosphere deep within Earth’s crust and offers the first example of a natural ecosystem that has its biological component entirely encoded within a single genome. The homogeneity of this genome is compatible with an ecosystem model in which relatively few generations have occurred since the emergence or isolation of this population. Given the age of the fracture water this would suggest a remarkably slow doubling time.

  17. Single-trial ERP analysis reveals facial expression category in a three-stage scheme.

    Science.gov (United States)

    Zhang, Dandan; Luo, Wenbo; Luo, Yuejia

    2013-05-28

    Emotional faces are salient stimuli that play a critical role in social interactions. Following up on previous research suggesting that the event-related potentials (ERPs) show differential amplitudes in response to various facial expressions, the current study used trial-to-trial variability assembled from six discriminating ERP components to predict the facial expression categories in individual trials. In an experiment involved 17 participants, fearful trials were differentiated from non-fearful trials as early as the intervals of N1 and P1, with a mean predictive accuracy of 87%. Single-trial features in the occurrence of N170 and vertex positive potential could distinguish between emotional and neutral expressions (accuracy=90%). Finally, the trials associated with fearful, happy, and neutral faces were completely separated during the window of N3 and P3 (accuracy=83%). These categorization findings elucidated the temporal evolution of facial expression extraction, and demonstrated that the spatio-temporal characteristics of single-trial ERPs can distinguish facial expressions according to a three-stage scheme, with "fear popup," "emotional/unemotional discrimination," and "complete separation" as processing stages. This work constitutes the first examination of neural processing dynamics beyond multitrial ERP averaging, and directly relates the prediction performance of single-trial classifiers to the progressive brain functions of emotional face discrimination.

  18. A Flow Cytometric Clonogenic Assay Reveals the Single-Cell Potency of Doxorubicin

    Science.gov (United States)

    Maass, Katie F.; Kulkarni, Chethana; Quadir, Mohiuddin A.; Hammond, Paula T.; Betts, Alison M.; Wittrup, K. Dane

    2015-01-01

    Standard cell proliferation assays use bulk media drug concentration to ascertain the potency of chemotherapeutic drugs; however, the relevant quantity is clearly the amount of drug actually taken up by the cell. To address this discrepancy, we have developed a flow cytometric clonogenic assay to correlate the amount of drug in a single cell with the cell’s ability to proliferate using a cell tracing dye and doxorubicin, a naturally fluorescent chemotherapeutic drug. By varying doxorubicin concentration in the media, length of treatment time, and treatment with verapamil, an efflux pump inhibitor, we introduced 105 – 1010 doxorubicin molecules per cell; then used a dye-dilution assay to simultaneously assess the number of cell divisions. We find that a cell’s ability to proliferate is a surprisingly conserved function of the number of intracellular doxorubicin molecules, resulting in single-cell IC50 values of 4 – 12 million intracellular doxorubicin molecules. The developed assay is a straightforward method for understanding a drug’s single-cell potency and can be used for any fluorescent or fluorescently-labeled drug, including nanoparticles or antibody-drug conjugates. PMID:26344409

  19. Evaluation of extremely small horizontal emittance

    Directory of Open Access Journals (Sweden)

    T. Okugi

    1999-02-01

    Full Text Available The KEK Accelerator Test Facility (KEK-ATF was constructed to develop technologies for producing a low-emittance beam which will be required by future linear colliders. The KEK-ATF consists of an injector linac, a damping ring, and a beam extraction line. The basic optical structure of the damping ring is a FOBO lattice, which reduces the horizontal dispersion at the center of the bending magnets and, as a consequence, can produce an extremely small emittance beam. To verify the performance of such a unique, low-emittance lattice, it is crucial to measure the horizontal emittance. The horizontal emittance was measured using wire scanners in the beam extraction line. Since the horizontal beam position was not stable, we established a method to correct the measured beam size for position fluctuation (“jitter” and we succeeded in the observation of the so far smallest horizontal emittance in any accelerator. The measured horizontal emittance was 1.37±0.03nm at a beam energy of 1.285 GeV and a bunch population of \\(3–5\\×10^{9}, in agreement with the design value of 1.27–1.34 nm at the beam energy and the bunch population.

  20. Optical characterization and modelling of paint top-coatings for low-emittance applications

    Science.gov (United States)

    Wäckelgård, Ewa; Svedung, Harald

    2016-09-01

    The study reports on characterization of low-infrared-emittance paint top-coatings for interior building applications in which the thermal radiation becomes important in comparison with thermal conductance. The top-coating that consist of a binder with aluminium flakes has been optically characterized in the infrared wavelength range in order to determine single flake and binder emittance from reflectance measurements. The single flake emittance was found to be 0.12 for non-leafing cornflake. The absorption coefficient that determines the binder emittance as a function of binder thickness was 0.060 [μm]-2 and 0.085 [μm]-2 for Lumiflon and polyester respectively. These results were used as parameters in a simple model of the flake-binder top-coating to investigate how the emittance of the top-coating was influence by the two components and compared with a state-of-art low-emittance commercial paint. It was found from the modelling that replacing the polyester binder with Lumiflon reduces the infrared emittance (at room temperature) from 0.36 to 0.30. Increasing flake reflectance from 0.88 to 0.96 and at the same time reduce flake thickness from 2 to 1 μm gives an emittance of 0.20. However, the real samples prepared with Lumiflon showed a severe degradation caused by the flakes floating up closer to the surface which indicates a viscosity problem that needs to be solved for practical use. Thinner flakes with higher reflectance can be found if vacuum metallised pigments are used instead of ball-milled.

  1. Stoichiometry and assembly of mTOR complexes revealed by single-molecule pulldown.

    Science.gov (United States)

    Jain, Ankur; Arauz, Edwin; Aggarwal, Vasudha; Ikon, Nikita; Chen, Jie; Ha, Taekjip

    2014-12-16

    The mammalian target of rapamycin (mTOR) kinase is a master regulator of cellular, developmental, and metabolic processes. Deregulation of mTOR signaling is implicated in numerous human diseases including cancer and diabetes. mTOR functions as part of either of the two multisubunit complexes, mTORC1 and mTORC2, but molecular details about the assembly and oligomerization of mTORCs are currently lacking. We use the single-molecule pulldown (SiMPull) assay that combines principles of conventional pulldown assays with single-molecule fluorescence microscopy to investigate the stoichiometry and assembly of mTORCs. After validating our approach with mTORC1, confirming a dimeric assembly as previously reported, we show that all major components of mTORC2 exist in two copies per complex, indicating that mTORC2 assembles as a homodimer. Interestingly, each mTORC component, when free from the complexes, is present as a monomer and no single subunit serves as the dimerizing component. Instead, our data suggest that dimerization of mTORCs is the result of multiple subunits forming a composite surface. SiMPull also allowed us to distinguish complex disassembly from stoichiometry changes. Physiological conditions that abrogate mTOR signaling such as nutrient deprivation or energy stress did not alter the stoichiometry of mTORCs. On the other hand, rapamycin treatment leads to transient appearance of monomeric mTORC1 before complete disruption of the mTOR-raptor interaction, whereas mTORC2 stoichiometry is unaffected. These insights into assembly of mTORCs may guide future mechanistic studies and exploration of therapeutic potential.

  2. Single-cell NF-kappaB dynamics reveal digital activation and analogue information processing.

    Science.gov (United States)

    Tay, Savaş; Hughey, Jacob J; Lee, Timothy K; Lipniacki, Tomasz; Quake, Stephen R; Covert, Markus W

    2010-07-08

    Cells operate in dynamic environments using extraordinary communication capabilities that emerge from the interactions of genetic circuitry. The mammalian immune response is a striking example of the coordination of different cell types. Cell-to-cell communication is primarily mediated by signalling molecules that form spatiotemporal concentration gradients, requiring cells to respond to a wide range of signal intensities. Here we use high-throughput microfluidic cell culture and fluorescence microscopy, quantitative gene expression analysis and mathematical modelling to investigate how single mammalian cells respond to different concentrations of the signalling molecule tumour-necrosis factor (TNF)-alpha, and relay information to the gene expression programs by means of the transcription factor nuclear factor (NF)-kappaB. We measured NF-kappaB activity in thousands of live cells under TNF-alpha doses covering four orders of magnitude. We find, in contrast to population-level studies with bulk assays, that the activation is heterogeneous and is a digital process at the single-cell level with fewer cells responding at lower doses. Cells also encode a subtle set of analogue parameters to modulate the outcome; these parameters include NF-kappaB peak intensity, response time and number of oscillations. We developed a stochastic mathematical model that reproduces both the digital and analogue dynamics as well as most gene expression profiles at all measured conditions, constituting a broadly applicable model for TNF-alpha-induced NF-kappaB signalling in various types of cells. These results highlight the value of high-throughput quantitative measurements with single-cell resolution in understanding how biological systems operate.

  3. Conformational Memory of a Protein Revealed by Single-Molecule Spectroscopy.

    Science.gov (United States)

    Schörner, Mario; Beyer, Sebastian Reinhardt; Southall, June; Cogdell, Richard J; Köhler, Jürgen

    2015-11-01

    Proteins are supramolecular machines that carry out a wide range of different functions, many of which require flexibility. Up until now spontaneous conformational fluctuations of proteins have always been assumed to reflect a stochastic random process. However, if changing between different conformational states was random, then it would be difficult to understand how conformational control of protein function could have evolved. Here we demonstrate that a single protein can show conformational memory. This is exactly the process that can facilitate the evolution of control of switching between two conformational states that can then be used to regulate protein function.

  4. Single, rapid coastal settlement of Asia revealed by analysis of complete mitochondrial genomes.

    Science.gov (United States)

    Macaulay, Vincent; Hill, Catherine; Achilli, Alessandro; Rengo, Chiara; Clarke, Douglas; Meehan, William; Blackburn, James; Semino, Ornella; Scozzari, Rosaria; Cruciani, Fulvio; Taha, Adi; Shaari, Norazila Kassim; Raja, Joseph Maripa; Ismail, Patimah; Zainuddin, Zafarina; Goodwin, William; Bulbeck, David; Bandelt, Hans-Jürgen; Oppenheimer, Stephen; Torroni, Antonio; Richards, Martin

    2005-05-13

    A recent dispersal of modern humans out of Africa is now widely accepted, but the routes taken across Eurasia are still disputed. We show that mitochondrial DNA variation in isolated "relict" populations in southeast Asia supports the view that there was only a single dispersal from Africa, most likely via a southern coastal route, through India and onward into southeast Asia and Australasia. There was an early offshoot, leading ultimately to the settlement of the Near East and Europe, but the main dispersal from India to Australia approximately 65,000 years ago was rapid, most likely taking only a few thousand years.

  5. Thermophotovoltaic emitter material selection and design

    Energy Technology Data Exchange (ETDEWEB)

    Saxton, P.C.; Moran, A.L.; Harper, M.J.; Lindler, K.W. [Naval Academy, Annapolis, MD (United States)

    1997-07-01

    Thermophotovoltaics (TPV) is a potentially attractive direct energy conversion technology. It reduces the need for complex machinery with moving parts and maintenance. TPV generators can be run from a variety of heat sources including waste heat for smaller scale operations. The US Naval Academy`s goal was to build a small experimental thermophotovoltaic generator powered by combustion gases from a General Electric T-58 helicopter gas turbine. The design of the generator imposes material limitations that directly affect emitter and structural materials selection. This paper details emitter material goals and requirements, and the methods used to select suitable candidate emitter materials for further testing.

  6. Laser wire emittance measurement line AT CLIC

    CERN Document Server

    Garcia, H; Blair, G A; Aumeyr, T; Schulte, D; Stulle, F

    2011-01-01

    A precise measurement of the transverse beam size and beam emittances upstream of the final focus is essential for ensuring the full luminosity at future linear colliders. A scheme for the emittance measurements at the RTML line of the CLIC using laser-wire beam profile monitors is described. A lattice of the measurement line is discussed and results of simulations of statistical errors and of their impact on the accuracy of the emittance reconstruction are given. Laser wire systems suitable for CLIC and their main characteristics are discussed.

  7. Single particle tracking reveals spatial and dynamic organization of the E. coli biofilm matrix.

    Science.gov (United States)

    Birjiniuk, Alona; Billings, Nicole; Nance, Elizabeth; Hanes, Justin; Ribbeck, Katharina; Doyle, Patrick S

    2014-08-27

    Biofilms are communities of surface-adherent bacteria surrounded by secreted polymers known as the extracellular polymeric substance (EPS). Biofilms are harmful in many industries, and thus it is of great interest to understand their mechanical properties and structure to determine ways to destabilize them. By performing single particle tracking with beads of varying surface functionalization it was found that charge interactions play a key role in mediating mobility within biofilms. With a combination of single particle tracking and microrheological concepts, it was found that Escherichia coli biofilms display height dependent charge density that evolves over time. Statistical analyses of bead trajectories and confocal microscopy showed inter-connecting micron scale channels that penetrate throughout the biofilm, which may be important for nutrient transfer through the system. This methodology provides significant insight into a particular biofilm system and can be applied to many others to provide comparisons of biofilm structure. The elucidation of structure provides evidence for the permeability of biofilms to microscale objects, and the ability of a biofilm to mature and change properties over time.

  8. Profiling single-guide RNA specificity reveals a mismatch sensitive core sequence

    Science.gov (United States)

    Zheng, Ting; Hou, Yingzi; Zhang, Pingjing; Zhang, Zhenxi; Xu, Ying; Zhang, Letian; Niu, Leilei; Yang, Yi; Liang, Da; Yi, Fan; Peng, Wei; Feng, Wenjian; Yang, Ying; Chen, Jianxin; Zhu, York Yuanyuan; Zhang, Li-He; Du, Quan

    2017-01-01

    Targeting specificity is an essential issue in the development of CRISPR-Cas technology. Using a luciferase activation assay, off-target cleavage activity of sgRNA was systematically investigated on single nucleotide-mismatched targets. In addition to confirming that PAM-proximal mismatches are less tolerated than PAM-distal mismatches, our study further identified a “core” sequence that is highly sensitive to target-mismatch. This sequence is of 4-nucleotide long, located at +4 to +7 position upstream of PAM, and positioned in a steric restriction region when assembled into Cas9 endonuclease. Our study also found that, single or multiple target mismatches at this region abolished off-target cleavage mediated by active sgRNAs, thus proposing a principle for gene-specific sgRNA design. Characterization of a mismatch sensitive “core” sequence not only enhances our understanding of how this elegant system functions, but also facilitates our efforts to improve targeting specificity of a sgRNA. PMID:28098181

  9. Single-cell RNAseq reveals cell adhesion molecule profiles in electrophysiologically defined neurons.

    Science.gov (United States)

    Földy, Csaba; Darmanis, Spyros; Aoto, Jason; Malenka, Robert C; Quake, Stephen R; Südhof, Thomas C

    2016-08-30

    In brain, signaling mediated by cell adhesion molecules defines the identity and functional properties of synapses. The specificity of presynaptic and postsynaptic interactions that is presumably mediated by cell adhesion molecules suggests that there exists a logic that could explain neuronal connectivity at the molecular level. Despite its importance, however, the nature of such logic is poorly understood, and even basic parameters, such as the number, identity, and single-cell expression profiles of candidate synaptic cell adhesion molecules, are not known. Here, we devised a comprehensive list of genes involved in cell adhesion, and used single-cell RNA sequencing (RNAseq) to analyze their expression in electrophysiologically defined interneurons and projection neurons. We compared the cell type-specific expression of these genes with that of genes involved in transmembrane ion conductances (i.e., channels), exocytosis, and rho/rac signaling, which regulates the actin cytoskeleton. Using these data, we identified two independent, developmentally regulated networks of interacting genes encoding molecules involved in cell adhesion, exocytosis, and signal transduction. Our approach provides a framework for a presumed cell adhesion and signaling code in neurons, enables correlating electrophysiological with molecular properties of neurons, and suggests avenues toward understanding synaptic specificity.

  10. Single-Molecule Imaging Reveals Topology Dependent Mutual Relaxation of Polymer Chains

    KAUST Repository

    Abadi, Maram

    2015-08-24

    The motion and relaxation of linear and cyclic polymers under entangled conditions are investigated by means of a newly developed single-molecule tracking technique, cumulative-area (CA) tracking. CA tracking enables simultaneous quantitative characterization of the diffusion mode, diffusion rate, and relaxation time that have been impossible with a widely used conventional single-molecule localization and tracking method, by analyzing cumulative areas occupied by the moving molecule. Using the novel approach, we investigate the motion and relaxation of entangled cyclic polymers, which have been an important but poorly understood question. Fluorescently labeled 42 kbp linear or cyclic tracer dsDNAs in concentrated solutions of unlabeled linear or cyclic DNAs are used as model systems. We show that CA tracking can explicitly distinguish topology-dependent diffusion mode, rate, and relaxation time, demonstrating that the method provides an invaluable tool for characterizing topological interaction between the entangled chains. We further demonstrate that the current models proposed for the entanglement between cyclic polymers which are based on cyclic chains moving through an array of fixed obstacles cannot correctly describe the motion of the cyclic chain under the entangled conditions. Our results rather suggest the mutual relaxation of the cyclic chains, which underscore the necessity of developing a new model to describe the motion of cyclic polymer under the entangled conditions based on the mutual interaction of the chains.

  11. Single molecule PCR reveals similar patterns of non-homologous DSB repair in tobacco and Arabidopsis.

    Directory of Open Access Journals (Sweden)

    Andrew H Lloyd

    Full Text Available DNA double strand breaks (DSBs occur constantly in eukaryotes. These potentially lethal DNA lesions are repaired efficiently by two major DSB repair pathways: homologous recombination and non-homologous end joining (NHEJ. We investigated NHEJ in Arabidopsis thaliana and tobacco (Nicotiana tabacum by introducing DNA double-strand breaks through inducible expression of I-SceI, followed by amplification of individual repair junction sequences by single-molecule PCR. Using this process over 300 NHEJ repair junctions were analysed in each species. In contrast to previously published variation in DSB repair between Arabidopsis and tobacco, the two species displayed similar DSB repair profiles in our experiments. The majority of repair events resulted in no loss of sequence and small (1-20 bp deletions occurred at a minority (25-45% of repair junctions. Approximately ~1.5% of the observed repair events contained larger deletions (>20 bp and a similar percentage contained insertions. Strikingly, insertion events in tobacco were associated with large genomic deletions at the site of the DSB that resulted in increased micro-homology at the sequence junctions suggesting the involvement of a non-classical NHEJ repair pathway. The generation of DSBs through inducible expression of I-SceI, in combination with single molecule PCR, provides an effective and efficient method for analysis of individual repair junctions and will prove a useful tool in the analysis of NHEJ.

  12. Landscape of Infiltrating T Cells in Liver Cancer Revealed by Single-Cell Sequencing.

    Science.gov (United States)

    Zheng, Chunhong; Zheng, Liangtao; Yoo, Jae-Kwang; Guo, Huahu; Zhang, Yuanyuan; Guo, Xinyi; Kang, Boxi; Hu, Ruozhen; Huang, Julie Y; Zhang, Qiming; Liu, Zhouzerui; Dong, Minghui; Hu, Xueda; Ouyang, Wenjun; Peng, Jirun; Zhang, Zemin

    2017-06-15

    Systematic interrogation of tumor-infiltrating lymphocytes is key to the development of immunotherapies and the prediction of their clinical responses in cancers. Here, we perform deep single-cell RNA sequencing on 5,063 single T cells isolated from peripheral blood, tumor, and adjacent normal tissues from six hepatocellular carcinoma patients. The transcriptional profiles of these individual cells, coupled with assembled T cell receptor (TCR) sequences, enable us to identify 11 T cell subsets based on their molecular and functional properties and delineate their developmental trajectory. Specific subsets such as exhausted CD8(+) T cells and Tregs are preferentially enriched and potentially clonally expanded in hepatocellular carcinoma (HCC), and we identified signature genes for each subset. One of the genes, layilin, is upregulated on activated CD8(+) T cells and Tregs and represses the CD8(+) T cell functions in vitro. This compendium of transcriptome data provides valuable insights and a rich resource for understanding the immune landscape in cancers. Copyright © 2017 Elsevier Inc. All rights reserved.

  13. Single molecule PCR reveals similar patterns of non-homologous DSB repair in tobacco and Arabidopsis.

    Science.gov (United States)

    Lloyd, Andrew H; Wang, Dong; Timmis, Jeremy N

    2012-01-01

    DNA double strand breaks (DSBs) occur constantly in eukaryotes. These potentially lethal DNA lesions are repaired efficiently by two major DSB repair pathways: homologous recombination and non-homologous end joining (NHEJ). We investigated NHEJ in Arabidopsis thaliana and tobacco (Nicotiana tabacum) by introducing DNA double-strand breaks through inducible expression of I-SceI, followed by amplification of individual repair junction sequences by single-molecule PCR. Using this process over 300 NHEJ repair junctions were analysed in each species. In contrast to previously published variation in DSB repair between Arabidopsis and tobacco, the two species displayed similar DSB repair profiles in our experiments. The majority of repair events resulted in no loss of sequence and small (1-20 bp) deletions occurred at a minority (25-45%) of repair junctions. Approximately ~1.5% of the observed repair events contained larger deletions (>20 bp) and a similar percentage contained insertions. Strikingly, insertion events in tobacco were associated with large genomic deletions at the site of the DSB that resulted in increased micro-homology at the sequence junctions suggesting the involvement of a non-classical NHEJ repair pathway. The generation of DSBs through inducible expression of I-SceI, in combination with single molecule PCR, provides an effective and efficient method for analysis of individual repair junctions and will prove a useful tool in the analysis of NHEJ.

  14. Single cell transcriptome analysis reveals dynamic changes in lncRNA expression during reprogramming

    Science.gov (United States)

    Kim, Daniel H.; Marinov, Georgi K.; Pepke, Shirley; Singer, Zakary S.; He, Peng; Williams, Brian; Schroth, Gary P.; Elowitz, Michael B.; Wold, Barbara J.

    2014-01-01

    SUMMARY Cellular reprogramming highlights the epigenetic plasticity of the somatic cell state. Long noncoding RNAs (lncRNAs) have emerging roles in epigenetic regulation, but their potential functions in reprogramming cell fate have been largely unexplored. We used single-cell RNA sequencing to characterize the expression patterns of over 16,000 genes, including 437 lncRNAs, during defined stages of reprogramming to pluripotency. Self-organizing maps (SOMs) were used as an intuitive way to structure and interrogate transcriptome data at the single-cell level. Early molecular events during reprogramming involved the activation of Ras signaling pathways, along with hundreds of lncRNAs. Loss-of-function studies showed that activated lncRNAs can repress lineage-specific genes, while lncRNAs activated in multiple reprogramming cell types can regulate metabolic gene expression. Our findings demonstrate that reprogramming cells activate defined sets of functionally relevant lncRNAs and provide a resource to further investigate how dynamic changes in the transcriptome reprogram cell state. PMID:25575081

  15. Single-cell RNA sequencing: revealing human pre-implantation development, pluripotency and germline development.

    Science.gov (United States)

    Petropoulos, S; Panula, S P; Schell, J P; Lanner, F

    2016-09-01

    Early human development is a dynamic, heterogeneous, complex and multidimensional process. During the first week, the single-cell zygote undergoes eight to nine rounds of cell division generating the multicellular blastocyst, which consists of hundreds of cells forming spatially organized embryonic and extra-embryonic tissues. At the level of transcription, degradation of maternal RNA commences at around the two-cell stage, coinciding with embryonic genome activation. Although numerous efforts have recently focused on delineating this process in humans, many questions still remain as thorough investigation has been limited by ethical issues, scarce availability of human embryos and the presence of minute amounts of DNA and RNA. In vitro cultures of embryonic stem cells provide some insight into early human development, but such studies have been confounded by analysis on a population level failing to appreciate cellular heterogeneity. Recent technical developments in single-cell RNA sequencing have provided a novel and powerful tool to explore the early human embryo in a systematic manner. In this review, we will discuss the advantages and disadvantages of the techniques utilized to specifically investigate human development and consider how the technology has yielded new insights into pre-implantation development, embryonic stem cells and the establishment of the germ line.

  16. Deep RNA sequencing at single base-pair resolution reveals high complexity of the rice transcriptome

    DEFF Research Database (Denmark)

    Zhang, Guojie; Guo, Guangwu; Hu, Xueda

    2010-01-01

    present the first transcriptome atlas for eight organs of cultivated rice. Using high-throughput paired-end RNA-seq, we unambiguously detected transcripts expressing at an extremely low level, as well as a substantial number of novel transcripts, exons, and untranslated regions. An analysis of alternative...... fusion events are more common than expected. In-depth analysis revealed a multitude of fusion transcripts that might be by-products of alternative splicing. Validation and chimeric transcript structural analysis provided evidence that some of these transcripts are likely to be functional in the cell...

  17. Nanosecond to submillisecond dynamics in dye-labeled single-stranded DNA, as revealed by ensemble measurements and photon statistics at single-molecule level.

    Science.gov (United States)

    Kaji, Takahiro; Ito, Syoji; Iwai, Shigenori; Miyasaka, Hiroshi

    2009-10-22

    Single-molecule and ensemble time-resolved fluorescence measurements were applied for the investigation of the conformational dynamics of single-stranded DNA, ssDNA, connected with a fluorescein dye by a C6 linker, where the motions both of DNA and the C6 linker affect the geometry of the system. From the ensemble measurement of the fluorescence quenching via photoinduced electron transfer with a guanine base in the DNA sequence, three main conformations were found in aqueous solution: a conformation unaffected by the guanine base in the excited state lifetime of fluorescein, a conformation in which the fluorescence is dynamically quenched in the excited-state lifetime, and a conformation leading to rapid quenching via nonfluorescent complex. The analysis by using the parameters acquired from the ensemble measurements for interphoton time distribution histograms and FCS autocorrelations by the single-molecule measurement revealed that interconversion in these three conformations took place with two characteristic time constants of several hundreds of nanoseconds and tens of microseconds. The advantage of the combination use of the ensemble measurements with the single-molecule detections for rather complex dynamic motions is discussed by integrating the experimental results with those obtained by molecular dynamics simulation.

  18. Tribology. Mechanisms of antiwear tribofilm growth revealed in situ by single-asperity sliding contacts.

    Science.gov (United States)

    Gosvami, N N; Bares, J A; Mangolini, F; Konicek, A R; Yablon, D G; Carpick, R W

    2015-04-03

    Zinc dialkyldithiophosphates (ZDDPs) form antiwear tribofilms at sliding interfaces and are widely used as additives in automotive lubricants. The mechanisms governing the tribofilm growth are not well understood, which limits the development of replacements that offer better performance and are less likely to degrade automobile catalytic converters over time. Using atomic force microscopy in ZDDP-containing lubricant base stock at elevated temperatures, we monitored the growth and properties of the tribofilms in situ in well-defined single-asperity sliding nanocontacts. Surface-based nucleation, growth, and thickness saturation of patchy tribofilms were observed. The growth rate increased exponentially with either applied compressive stress or temperature, consistent with a thermally activated, stress-assisted reaction rate model. Although some models rely on the presence of iron to catalyze tribofilm growth, the films grew regardless of the presence of iron on either the tip or substrate, highlighting the critical role of stress and thermal activation.

  19. Single-molecule microscopy reveals heterogeneous dynamics of lipid raft components upon TCR engagement.

    Science.gov (United States)

    Drbal, Karel; Moertelmaier, Manuel; Holzhauser, Christa; Muhammad, Arshad; Fuertbauer, Elke; Howorka, Stefan; Hinterberger, Maria; Stockinger, Hannes; Schütz, Gerhard J

    2007-05-01

    The existence of lipid rafts and their importance for immunoreceptor signaling is highly debated. By non-invasive single molecule imaging, we analyzed the dynamics of the T-cell antigen receptor (TCR), the lipid raft-associated glycosylphosphatidylinositol (GPI) proteins CD48 and CD59 and the major leukocyte phosphatase CD45 in living naive T lymphocytes. TCR triggering induced the immobilization of CD45 and CD48 at different positions within the T-cell interface. The second GPI protein, CD59, did not co-immobilize indicating lipid raft heterogeneity in living T lymphocytes. A novel biochemical approach confirmed that lipid raft components are not associated in the plasma membrane of resting cells, and variably associate with specific receptors to distinct lipid rafts upon activation.

  20. Single-cell RNA sequencing reveals molecular and functional platelet bias of aged haematopoietic stem cells.

    Science.gov (United States)

    Grover, Amit; Sanjuan-Pla, Alejandra; Thongjuea, Supat; Carrelha, Joana; Giustacchini, Alice; Gambardella, Adriana; Macaulay, Iain; Mancini, Elena; Luis, Tiago C; Mead, Adam; Jacobsen, Sten Eirik W; Nerlov, Claus

    2016-03-24

    Aged haematopoietic stem cells (HSCs) generate more myeloid cells and fewer lymphoid cells compared with young HSCs, contributing to decreased adaptive immunity in aged individuals. However, it is not known how intrinsic changes to HSCs and shifts in the balance between biased HSC subsets each contribute to the altered lineage output. Here, by analysing HSC transcriptomes and HSC function at the single-cell level, we identify increased molecular platelet priming and functional platelet bias as the predominant age-dependent change to HSCs, including a significant increase in a previously unrecognized class of HSCs that exclusively produce platelets. Depletion of HSC platelet programming through loss of the FOG-1 transcription factor is accompanied by increased lymphoid output. Therefore, increased platelet bias may contribute to the age-associated decrease in lymphopoiesis.

  1. A heterotrimer model of the complete Microprocessor complex revealed by single-molecule subunit counting.

    Science.gov (United States)

    Herbert, Kristina M; Sarkar, Susanta K; Mills, Maria; Delgado De la Herran, Hilda C; Neuman, Keir C; Steitz, Joan A

    2016-02-01

    During microRNA (miRNA) biogenesis, the Microprocessor complex (MC), composed minimally of Drosha, an RNaseIII enzyme, and DGCR8, a double-stranded RNA-binding protein, cleaves the primary-miRNA (pri-miRNA) to release the pre-miRNA stem-loop structure. Size-exclusion chromatography of the MC, isolated from mammalian cells, suggested multiple copies of one or both proteins in the complex. However, the exact stoichiometry was unknown. Initial experiments suggested that DGCR8 bound pri-miRNA substrates specifically, and given that Drosha could not be bound or cross-linked to RNA, a sequential model for binding was established in which DGCR8 bound first and recruited Drosha. Therefore, many laboratories have studied DGCR8 binding to RNA in the absence of Drosha and have shown that deletion constructs of DGCR8 can multimerize in the presence of RNA. More recently, it was demonstrated that Drosha can bind pri-miRNA substrates in the absence of DGCR8, casting doubt on the sequential model of binding. In the same study, using a single-molecule photobleaching assay, fluorescent protein-tagged deletion constructs of DGCR8 and Drosha assembled into a heterotrimeric complex on RNA, comprising two DGCR8 molecules and one Drosha molecule. To determine the stoichiometry of Drosha and DGCR8 within the MC in the absence of added RNA, we also used a single-molecule photobleaching assay and confirmed the heterotrimeric model of the human MC. We demonstrate that a heterotrimeric complex is likely preformed in the absence of RNA and exists even when full-length proteins are expressed and purified from human cells, and when hAGT-derived tags are used rather than fluorescent proteins.

  2. Single-molecule dynamics reveals cooperative binding-folding in protein recognition.

    Directory of Open Access Journals (Sweden)

    Jin Wang

    2006-07-01

    Full Text Available The study of associations between two biomolecules is the key to understanding molecular function and recognition. Molecular function is often thought to be determined by underlying structures. Here, combining a single-molecule study of protein binding with an energy-landscape-inspired microscopic model, we found strong evidence that biomolecular recognition is determined by flexibilities in addition to structures. Our model is based on coarse-grained molecular dynamics on the residue level with the energy function biased toward the native binding structure (the Go model. With our model, the underlying free-energy landscape of the binding can be explored. There are two distinct conformational states at the free-energy minimum, one with partial folding of CBD itself and significant interface binding of CBD to Cdc42, and the other with native folding of CBD itself and native interface binding of CBD to Cdc42. This shows that the binding process proceeds with a significant interface binding of CBD with Cdc42 first, without a complete folding of CBD itself, and that binding and folding are then coupled to reach the native binding state. The single-molecule experimental finding of dynamic fluctuations among the loosely and closely bound conformational states can be identified with the theoretical, calculated free-energy minimum and explained quantitatively in the model as a result of binding associated with large conformational changes. The theoretical predictions identified certain key residues for binding that were consistent with mutational experiments. The combined study identified fundamental mechanisms and provided insights about designing and further exploring biomolecular recognition with large conformational changes.

  3. Single-cell analysis reveals gene-expression heterogeneity in syntrophic dual-culture of Desulfovibrio vulgaris with Methanosarcina barkeri

    Science.gov (United States)

    Qi, Zhenhua; Pei, Guangsheng; Chen, Lei; Zhang, Weiwen

    2014-12-01

    Microbial syntrophic metabolism has been well accepted as the heart of how methanogenic and other anaerobic microbial communities function. In this work, we applied a single-cell RT-qPCR approach to reveal gene-expression heterogeneity in a model syntrophic system of Desulfovibrio vulgaris and Methanosarcina barkeri, as compared with the D. vulgaris monoculture. Using the optimized primers and single-cell analytical protocol, we quantitatively determine gene-expression levels of 6 selected target genes in each of the 120 single cells of D. vulgaris isolated from its monoculture and dual-culture with M. barkeri. The results demonstrated very significant cell-to-cell gene-expression heterogeneity for the selected D. vulgaris genes in both the monoculture and the syntrophic dual-culture. Interestingly, no obvious increase in gene-expression heterogeneity for the selected genes was observed for the syntrophic dual-culture when compared with its monoculture, although the community structure and cell-cell interactions have become more complicated in the syntrophic dual-culture. In addition, the single-cell RT-qPCR analysis also provided further evidence that the gene cluster (DVU0148-DVU0150) may be involved syntrophic metabolism between D. vulgaris and M. barkeri. Finally, the study validated that single-cell RT-qPCR analysis could be a valuable tool in deciphering gene functions and metabolism in mixed-cultured microbial communities.

  4. Improved Rare-Earth Emitter Hollow Cathode

    Science.gov (United States)

    Goebel, Dan M.

    2011-01-01

    An improvement has been made to the design of the hollow cathode geometry that was created for the rare-earth electron emitter described in Compact Rare Earth Emitter Hollow Cathode (NPO-44923), NASA Tech Briefs, Vol. 34, No. 3 (March 2010), p. 52. The original interior assembly was made entirely of graphite in order to be compatible with the LaB6 material, which cannot be touched by metals during operation due to boron diffusion causing embrittlement issues in high-temperature refractory materials. Also, the graphite tube was difficult to machine and was subject to vibration-induced fracturing. This innovation replaces the graphite tube with one made out of refractory metal that is relatively easy to manufacture. The cathode support tube is made of molybdenum or molybdenum-rhenium. This material is easily gun-bored to near the tolerances required, and finish machined with steps at each end that capture the orifice plate and the mounting flange. This provides the manufacturability and robustness needed for flight applications, and eliminates the need for expensive e-beam welding used in prior cathodes. The LaB6 insert is protected from direct contact with the refractory metal tube by thin, graphite sleeves in a cup-arrangement around the ends of the insert. The sleeves, insert, and orifice plate are held in place by a ceramic spacer and tungsten spring inserted inside the tube. To heat the cathode, an insulating tube is slipped around the refractory metal hollow tube, which can be made of high-temperature materials like boron nitride or aluminum nitride. A screw-shaped slot, or series of slots, is machined in the outside of the ceramic tube to constrain a refractory metal wire wound inside the slot that is used as the heater. The screw slot can hold a single heater wire that is then connected to the front of the cathode tube by tack-welding to complete the electrical circuit, or it can be a double slot that takes a bifilar wound heater with both leads coming out

  5. Flexible control of femtosecond pulse duration and separation using an emittance-spoiling foil in x-ray free-electron lasers

    Energy Technology Data Exchange (ETDEWEB)

    Ding, Y. [SLAC National Accelerator Lab., Menlo Park, CA (United States); Behrens, C. [Deutsches Elektronen-Synchrotron (DESY), Hamburg (Germany); Coffee, R. [SLAC National Accelerator Lab., Menlo Park, CA (United States); Decker, F. -J. [SLAC National Accelerator Lab., Menlo Park, CA (United States); Emma, P. [SLAC National Accelerator Lab., Menlo Park, CA (United States); Field, C. [SLAC National Accelerator Lab., Menlo Park, CA (United States); Helml, W. [Technische Univ. Munchen, Garching (Germany); Huang, Z. [SLAC National Accelerator Lab., Menlo Park, CA (United States); Krejcik, P. [SLAC National Accelerator Lab., Menlo Park, CA (United States); Krzywinski, J. [SLAC National Accelerator Lab., Menlo Park, CA (United States); Loos, H. [SLAC National Accelerator Lab., Menlo Park, CA (United States); Lutman, A. [SLAC National Accelerator Lab., Menlo Park, CA (United States); Marinelli, A. [SLAC National Accelerator Lab., Menlo Park, CA (United States); Maxwell, T. J. [SLAC National Accelerator Lab., Menlo Park, CA (United States); Turner, J. [SLAC National Accelerator Lab., Menlo Park, CA (United States)

    2015-06-22

    We report experimental studies of generating and controlling femtosecond x-ray pulses in free-electron lasers (FELs) using an emittance spoiling foil. By selectivity spoiling the transverse emittance of the electron beam, the output pulse duration or double-pulse separation is adjusted with a variable size single or double slotted foil. Measurements were performed with an X-band transverse deflector located downstream of the FEL undulator, from which both the FEL lasing and emittance spoiling effects are observed directly.

  6. The Next Generation Photoinjector (thermal Emittance, Quantum Efficiency)

    CERN Document Server

    Palmer, D T

    1998-01-01

    This dissertation will elucidate the design, construction, theory, and operation of the Next Generation Photoinjector (NGP). This photoinjector is comprised of the BNL/SLAC/UCLA 1.6 cell symmetrized S-band photocathode radio frequency (rf) electron gun and a single emittance-compensation solenoidal magnet. This photoinjector is a prototype for the Linear Coherent Light Source X-ray Free Electron Laser operating in the 1.5 A range. Simulations indicate that this photoinjector is capable of producing a 1 nC electron bunch with transverse normalized emittance less than 1 $\\pi$ mm-mrad were the cathode is illuminated with a 10 psec longitudinal flat top pulse. Using a Gaussian longitudinal laser profile with a full width half maximum (FWHM) of 10 psec, simulation indicates that the NGP is capable of producing a normalized rms emittance of 2.50 $\\pi$ mm-mrad at 1 nC. Using the removable cathode plate we have studied the quantum efficiency (QE) of both copper and magnesium photo-cathodes...

  7. Beam emittance measurements on multicusp ion sources

    Energy Technology Data Exchange (ETDEWEB)

    Sarstedt, M.; Lee, Y.; Leung, K.N.; Perkins, L.T.; Pickard, D.S.; Weber, M.; Williams, M.D.

    1995-08-01

    Multicusp ion sources are used for various applications. Presently, the implementation of this type of ion source is planned for the development of an ion beam lithography machine, which will be used for the projection of sub-0.2 micron patterns onto a wafer substrate. Since, for this application, a very good beam quality and a small ion energy spread are required, emittance measurements have been performed on a multicusp ion source for various source conditions. It is shown that the installation of proper capacitors between the extraction electrodes is necessary to avoid rf-pickup, which otherwise leads to a distortion of the beam emittance. The influence of the magnetic filter field on the beam emittance has been investigated, and the beam emittance of a dc filament-discharge plasma has also been compared to that of an rf-generated plasma.

  8. Beam emittance measurements on multicusp ion sources

    Energy Technology Data Exchange (ETDEWEB)

    Sarstedt, M.; Lee, Y.; Leung, K.N. [and others

    1995-08-01

    Multicusp ion sources are used for various applications. Presently, the implementation of this type of ion source planned for the development of an ion beam lithography machine, which will be used for the projection of sub-0.2 {mu}m patterns onto a wafer substrate. Since, for this application, a very good beam quality and a small ion energy spread are required, emittance measurements have been performed on a multicusp ion source for various source conditions. It is shown that the installation of proper capacitors between the extraction electrodes is necessary to avoid rf-pickup, which otherwise leads to a distortion of the beam emittance. The influence of the magnetic filter field on the beam emittance has been investigated, and the beam emittance of a dc filament-discharge plasma has also been compared to that of an rf-generated plasma.

  9. Beam emittance measurements on multicusp ion sources

    Energy Technology Data Exchange (ETDEWEB)

    Sarstedt, M.; Lee, Y.; Leung, K.N.; Perkins, L.T.; Pickard, D.S.; Weber, M.; Williams, M.D. [Lawrence Berkeley National Laboratory, University of California, Berkeley, California 94720 (United States)

    1996-03-01

    Multicusp ion sources are used for various applications. Presently, the implementation of this type of ion source is planned for the development of an ion beam lithography machine, which will be used for the projection of sub-0.2 {mu}m patterns onto a wafer substrate. Since, for this application, a very good beam quality and a small ion energy spread are required, emittance measurements have been performed on a multicusp ion source for various source conditions. It is shown that the installation of proper capacitors between the extraction electrodes is necessary to avoid rf pickup, which otherwise leads to a distortion of the beam emittance. The influence of the magnetic filter field on the beam emittance has been investigated, and the beam emittance of a dc filament-discharge plasma has also been compared to that of a rf-generated plasma. {copyright} {ital 1996 American Institute of Physics.}

  10. Beam emittance measurements on multicusp ion sources

    Science.gov (United States)

    Sarstedt, M.; Lee, Y.; Leung, K. N.; Perkins, L. T.; Pickard, D. S.; Weber, M.; Williams, M. D.

    1996-03-01

    Multicusp ion sources are used for various applications. Presently, the implementation of this type of ion source is planned for the development of an ion beam lithography machine, which will be used for the projection of sub-0.2 μm patterns onto a wafer substrate. Since, for this application, a very good beam quality and a small ion energy spread are required, emittance measurements have been performed on a multicusp ion source for various source conditions. It is shown that the installation of proper capacitors between the extraction electrodes is necessary to avoid rf pickup, which otherwise leads to a distortion of the beam emittance. The influence of the magnetic filter field on the beam emittance has been investigated, and the beam emittance of a dc filament-discharge plasma has also been compared to that of a rf-generated plasma.

  11. Monochromatic gamma emitter for low energy quanta

    CERN Document Server

    Tomova, Z R; Mironova, S A

    2004-01-01

    The possibility of creating of a monochromatic gamma emitter of low energy quanta is analyzed. The idea is based on Daning's scheme. Except for purely scientific problems the monochromator is actual for therapy of wide range of diseases.

  12. Emittance growth in linear induction accelerators

    CERN Document Server

    Ekdahl, C A; Schulze, M E; Carlson, C A; Frayer, D K; Mostrum, C; Thoma, C H

    2014-01-01

    The Dual-Axis Radiographic Hydrotest (DARHT) facility uses bremsstrahlung radiation source spots produced by the focused electron beams from two linear induction accelerators (LIAs) to radiograph large hydrodynamic experiments driven by high explosives. Radiographic resolution is determined by the size of the source spot, and beam emittance is the ultimate limitation to spot size. On the DARHT Axis-II LIA we measure an emittance higher than predicted by theoretical simulations, and even though this axis produces sub-millimeter source spots, we are exploring ways to improve the emittance. Some of the possible causes for the discrepancy have been investigated using particle-in-cell (PIC) codes, although most of these are discounted based on beam measurements. The most likely source of emittance growth is a mismatch of the beam to the magnetic transport, which can cause beam halo.

  13. Emittance Growth in Linear Induction Accelerators

    OpenAIRE

    Ekdahl, Carl

    2017-01-01

    The Dual-Axis Radiographic Hydrotest (DARHT) facility uses bremsstrahlung radiation source spots produced by the focused electron beams from two linear induction accelerators (LIAs) to radiograph large hydrodynamic experiments driven by high explosives. Radiographic resolution is determined by the size of the source spot, and beam emittance is the ultimate limitation to spot size. Some of the possible causes for the emittance growth in the DARHT LIA have been investigated using particle-in-ce...

  14. Alpha-emitters for medical therapy workshop

    Energy Technology Data Exchange (ETDEWEB)

    Feinendegen, L.E.; McClure, J.J.

    1996-12-31

    A workshop on ``Alpha-Emitters for Medical Therapy`` was held May 30-31, 1996 in Denver Colorado to identify research goals and potential clinical needs for applying alpha-particle emitters and to provide DOE with sufficient information for future planning. The workshop was attended by 36 participants representing radiooncology, nuclear medicine, immunotherapy, radiobiology, molecular biology, biochemistry, radiopharmaceutical chemistry, dosimetry, and physics. This report provides a summary of the key points and recommendations arrived at during the conference.

  15. Charged single alpha-helices in proteomes revealed by a consensus prediction approach.

    Science.gov (United States)

    Gáspári, Zoltán; Süveges, Dániel; Perczel, András; Nyitray, László; Tóth, Gábor

    2012-04-01

    Charged single α-helices (CSAHs) constitute a recently recognized protein structural motif. Its presence and role is characterized in only a few proteins. To explore its general features, a comprehensive study is necessary. We have set up a consensus prediction method available as a web service (at http://csahserver.chem.elte.hu) and downloadable scripts capable of predicting CSAHs from protein sequences. Using our method, we have performed a comprehensive search on the UniProt database. We found that the motif is very rare but seems abundant in proteins involved in symbiosis and RNA binding/processing. Although there are related proteins with CSAH segments, the motif shows no deep conservation in protein families. We conclude that CSAH-containing proteins, although rare, are involved in many key biological processes. Their conservation pattern and prevalence in symbiosis-associated proteins suggest that they might be subjects of relatively rapid molecular evolution and thus can contribute to the emergence of novel functions.

  16. Coherent energy scale revealed by ultrafast dynamics of UX3 (X = Al, Sn, Ga) single crystals

    Science.gov (United States)

    Nair, Saritha K.; Zhu, J.-X.; Sarrao, J. L.; Taylor, A. J.; Chia, Elbert E. M.

    2012-09-01

    The temperature dependence of relaxation dynamics of UX3 (X = Al, Ga, Sn) compounds is studied using the time-resolved pump-probe technique in reflectance geometry. For UGa3, our data are consistent with the formation of a spin density wave gap as evidenced from the quasidivergence of the relaxation time τ near the Néel temperature TN. For UAl3 and USn3, the relaxation dynamics shows a change from single-exponential to two-exponential behavior below a particular temperature, suggestive of coherence formation of the 5f electrons with the conduction band electrons. This particular temperature can be attributed to the spin fluctuation temperature Tsf, a measure of the strength of Kondo coherence. Our Tsf is consistent with other data such as resistivity and susceptibility measurements. The temperature dependence of the relaxation amplitude and time of UAl3 and USn3 were also fitted by the Rothwarf-Taylor model. Our results show that ultrafast optical spectroscopy is sensitive to c-f Kondo hybridization in the f-electron systems.

  17. Metabolic diversity and ecological niches of Achromatium populations revealed with single-cell genomic sequencing

    Directory of Open Access Journals (Sweden)

    Muammar eMansor

    2015-08-01

    Full Text Available Large, sulfur-cycling, calcite-precipitating bacteria in the genus Achromatium represent a significant proportion of bacterial communities near sediment-water interfaces throughout the world. Our understanding of their potentially crucial roles in calcium, carbon, sulfur, nitrogen, and iron cycling is limited because they have not been cultured or sequenced using environmental genomics approaches to date. We utilized single-cell genomic sequencing to obtain one incomplete and two nearly complete draft genomes for Achromatium collected at Warm Mineral Springs, FL. Based on 16S rRNA gene sequences, the three cells represent distinct and relatively distant Achromatium populations (91-92% identity. The draft genomes encode key genes involved in sulfur and hydrogen oxidation; oxygen, nitrogen and polysulfide respiration; carbon and nitrogen fixation; organic carbon assimilation and storage; chemotaxis; twitching motility; antibiotic resistance; and membrane transport. Known genes for iron and manganese energy metabolism were not detected. The presence of pyrophosphatase and vacuolar (V-type ATPases, which are generally rare in bacterial genomes, suggests a role for these enzymes in calcium transport, proton pumping, and/or energy generation in the membranes of calcite-containing inclusions.

  18. Single-cell spatial reconstruction reveals global division of labour in the mammalian liver.

    Science.gov (United States)

    Bahar Halpern, Keren; Shenhav, Rom; Matcovitch-Natan, Orit; Tóth, Beáta; Lemze, Doron; Golan, Matan; Massasa, Efi E; Baydatch, Shaked; Landen, Shanie; Moor, Andreas E; Brandis, Alexander; Giladi, Amir; Stokar-Avihail, Avigail; David, Eyal; Amit, Ido; Itzkovitz, Shalev

    2017-02-16

    The mammalian liver consists of hexagon-shaped lobules that are radially polarized by blood flow and morphogens. Key liver genes have been shown to be differentially expressed along the lobule axis, a phenomenon termed zonation, but a detailed genome-wide reconstruction of this spatial division of labour has not been achieved. Here we measure the entire transcriptome of thousands of mouse liver cells and infer their lobule coordinates on the basis of a panel of zonated landmark genes, characterized with single-molecule fluorescence in situ hybridization. Using this approach, we obtain the zonation profiles of all liver genes with high spatial resolution. We find that around 50% of liver genes are significantly zonated and uncover abundant non-monotonic profiles that peak at the mid-lobule layers. These include a spatial order of bile acid biosynthesis enzymes that matches their position in the enzymatic cascade. Our approach can facilitate the reconstruction of similar spatial genomic blueprints for other mammalian organs.

  19. Overcoming computational uncertainties to reveal chemical sensitivity in single molecule conduction calculations.

    Science.gov (United States)

    Solomon, Gemma C; Reimers, Jeffrey R; Hush, Noel S

    2005-06-01

    In the calculation of conduction through single molecule's approximations about the geometry and electronic structure of the system are usually made in order to simplify the problem. Previously [G. C. Solomon, J. R. Reimers, and N. S. Hush, J. Chem. Phys. 121, 6615 (2004)], we have shown that, in calculations employing cluster models for the electrodes, proper treatment of the open-shell nature of the clusters is the most important computational feature required to make the results sensitive to variations in the structural and chemical features of the system. Here, we expand this and establish a general hierarchy of requirements involving treatment of geometrical approximations. These approximations are categorized into two classes: those associated with finite-dimensional methods for representing the semi-infinite electrodes, and those associated with the chemisorption topology. We show that ca. 100 unique atoms are required in order to properly characterize each electrode: using fewer atoms leads to nonsystematic variations in conductivity that can overwhelm the subtler changes. The choice of binding site is shown to be the next most important feature, while some effects that are difficult to control experimentally concerning the orientations at each binding site are actually shown to be insignificant. Verification of this result provides a general test for the precision of computational procedures for molecular conductivity. Predictions concerning the dependence of conduction on substituent and other effects on the central molecule are found to be meaningful only when they exceed the uncertainties of the effects associated with binding-site variation.

  20. Imaging single endocytic events reveals diversity in clathrin, dynamin and vesicle dynamics.

    Science.gov (United States)

    Mattheyses, Alexa L; Atkinson, Claire E; Simon, Sanford M

    2011-10-01

    The dynamics of clathrin-mediated endocytosis can be assayed using fluorescently tagged proteins and total internal reflection fluorescence microscopy. Many of these proteins, including clathrin and dynamin, are soluble and changes in fluorescence intensity can be attributed either to membrane/vesicle movement or to changes in the numbers of individual molecules. It is important for assays to discriminate between physical membrane events and the dynamics of molecules. Two physical events in endocytosis were investigated: vesicle scission from the plasma membrane and vesicle internalization. Single vesicle analysis allowed the characterization of dynamin and clathrin dynamics relative to scission and internalization. We show that vesicles remain proximal to the plasma membrane for variable amounts of time following scission, and that uncoating of clathrin can occur before or after vesicle internalization. The dynamics of dynamin also vary with respect to scission. Results from assays based on physical events suggest that disappearance of fluorescence from the evanescent field should be re-evaluated as an assay for endocytosis. These results illustrate the heterogeneity of behaviors of endocytic vesicles and the importance of establishing suitable evaluation criteria for biophysical processes.

  1. Intestinal crypt homeostasis revealed at single-stem-cell level by in vivo live imaging

    Science.gov (United States)

    Ritsma, Laila; Ellenbroek, Saskia I. J.; Zomer, Anoek; Snippert, Hugo J.; de Sauvage, Frederic J.; Simons, Benjamin D.; Clevers, Hans; van Rheenen, Jacco

    2014-03-01

    The rapid turnover of the mammalian intestinal epithelium is supported by stem cells located around the base of the crypt. In addition to the Lgr5 marker, intestinal stem cells have been associated with other markers that are expressed heterogeneously within the crypt base region. Previous quantitative clonal fate analyses have led to the proposal that homeostasis occurs as the consequence of neutral competition between dividing stem cells. However, the short-term behaviour of individual Lgr5+ cells positioned at different locations within the crypt base compartment has not been resolved. Here we establish the short-term dynamics of intestinal stem cells using the novel approach of continuous intravital imaging of Lgr5-Confetti mice. We find that Lgr5+ cells in the upper part of the niche (termed `border cells') can be passively displaced into the transit-amplifying domain, after the division of proximate cells, implying that the determination of stem-cell fate can be uncoupled from division. Through quantitative analysis of individual clonal lineages, we show that stem cells at the crypt base, termed `central cells', experience a survival advantage over border stem cells. However, through the transfer of stem cells between the border and central regions, all Lgr5+ cells are endowed with long-term self-renewal potential. These findings establish a novel paradigm for stem-cell maintenance in which a dynamically heterogeneous cell population is able to function long term as a single stem-cell pool.

  2. Uncoating Mechanism of Carnation Mottle Virus Revealed by Cryo-EM Single Particle Analysis.

    Science.gov (United States)

    Wang, Chun-Yan; Zhang, Qin-Fen; Gao, Yuan-Zhu; Xie, Li; Li, Hong-Mei; Hong, Jian; Zhang, Chuan-Xi

    2015-01-01

    Genome uncoating is a prerequisite for the successful infection of plant viruses in host plants. Thus far, little is known about the genome uncoating of the Carnation mottle virus (CarMV). Here, we obtained two reconstructions of CarMV at pH7 in the presence (Ca-pH7) and absence (EDTA-pH7) of calcium ions by Cryo-EM single particle analysis, which achieved 6.4 Å and 8 Å resolutions respectively. Our results showed that chelation of the calcium ions under EDTA-pH7 resulted in reduced interaction between the subunits near the center of the asymmetric unit but not overall size change of the viral particles, which indicated that the role of the calcium ions in CarMV was not predominantly for the structural preservation. Part of the genomic RNA closest to the capsid was found to be located near the center of the asymmetric unit, which might result from the interaction between genomic RNA and Lys194 residues. Together with the electrostatic potential analysis on the inner surface of the asymmetric unit, the reduced interaction near the center of the asymmetric unit under EDTA-pH7 suggested that the genome release of CarMV might be realized through the center of the asymmetric unit.

  3. Collinear antiferromagnetism in trigonal SrMn2As2 revealed by single crystal neutron diffraction

    Science.gov (United States)

    Kreyssig, A.; Das, P.; Sangeetha, N. S.; Benson, Z. A.; Heitman, T.; Johnston, D. C.; Goldman, A. I.

    FeAs-based compounds and related materials have been an area of intense research in understanding the complex interplay between magnetism and superconductivity. Here we report on the magnetic structure of SrMn2As2 that crystallizes in a trigonal structure (P 3 m1) and undergoes an antiferromagnetic (AFM) transition at TN ~ 120 K. The temperature dependence of the magnetic susceptibility remains nearly constant below TN with H ∥ c while it decreases significantly with H ∥ ab . This shows that the local Mn moments order and lie in the ab plane instead of aligning along the c axis as in BaMn2As2. Single crystal neutron diffraction measurements on SrMn2As2 determined that the Mn moments are collinearly aligned in a G-type AFM order with AFM alignments between a moment and all nearest neighbors in the basal plane and also perpendicular to it. This manifests that G-type AFM order is robust for Mn122 systems despite different symmetries, i.e. tetragonal for BaMn2As2 and trigonal for SrMn2As2.Work at Ames Laboratory was supported by the DOE, BES, Division of Materials Sciences & Engineering, through DE-AC02-07CH11358. This research used resources at University of Missouri Research Reactor.

  4. Insights into the genome of large sulfur bacteria revealed by analysis of single filaments.

    Directory of Open Access Journals (Sweden)

    Marc Mussmann

    2007-09-01

    Full Text Available Marine sediments are frequently covered by mats of the filamentous Beggiatoa and other large nitrate-storing bacteria that oxidize hydrogen sulfide using either oxygen or nitrate, which they store in intracellular vacuoles. Despite their conspicuous metabolic properties and their biogeochemical importance, little is known about their genetic repertoire because of the lack of pure cultures. Here, we present a unique approach to access the genome of single filaments of Beggiatoa by combining whole genome amplification, pyrosequencing, and optical genome mapping. Sequence assemblies were incomplete and yielded average contig sizes of approximately 1 kb. Pathways for sulfur oxidation, nitrate and oxygen respiration, and CO2 fixation confirm the chemolithoautotrophic physiology of Beggiatoa. In addition, Beggiatoa potentially utilize inorganic sulfur compounds and dimethyl sulfoxide as electron acceptors. We propose a mechanism of vacuolar nitrate accumulation that is linked to proton translocation by vacuolar-type ATPases. Comparative genomics indicates substantial horizontal gene transfer of storage, metabolic, and gliding capabilities between Beggiatoa and cyanobacteria. These capabilities enable Beggiatoa to overcome non-overlapping availabilities of electron donors and acceptors while gliding between oxic and sulfidic zones. The first look into the genome of these filamentous sulfur-oxidizing bacteria substantially deepens the understanding of their evolution and their contribution to sulfur and nitrogen cycling in marine sediments.

  5. Indentation Size Effects in Single Crystal Copper as Revealed by Synchrotron X-ray Microdiffraction

    Energy Technology Data Exchange (ETDEWEB)

    Feng, G.; Budiman, A. S.; Nix, W. D.; Tamura, N.; Patel, J. R.

    2007-11-19

    The indentation size effect (ISE) has been observed in numerous nanoindentation studies on crystalline materials; it is found that the hardness increases dramatically with decreasing indentation size - a 'smaller is stronger' phenomenon. Some have attributed the ISE to the existence of strain gradients and the geometrically necessary dislocations (GNDs). Since the GND density is directly related to the local lattice curvature, the Scanning X-ray Microdiffraction ({mu}SXRD) technique, which can quantitatively measure relative lattice rotations through the streaking of Laue diffractions, can used to study the strain gradients. The synchrotron {mu}SXRD technique we use - which was developed at the Advanced Light Source (ALS), Berkeley Lab - allows for probing the local plastic behavior of crystals with sub-micrometer resolution. Using this technique, we studied the local plasticity for indentations of different depths in a Cu single crystal. Broadening of Laue diffractions (streaking) was observed, showing local crystal lattice rotation due to the indentation-induced plastic deformation. A quantitative analysis of the streaking allows us to estimate the average GND density in the indentation plastic zones. The size dependence of the hardness, as found by nanoindentation, will be described, and its correlation to the observed lattice rotations will be discussed.

  6. Single micelle force microscopy reveals the coordination interaction between catechol and Fe33+

    Science.gov (United States)

    Li, Yiran; Cao, Yi; Wang, Wei

    Metal coordination bonds are widely found in natural adhesive, load-bearing, and protective materials, which are thought to be responsible for their high strength and toughness. However, it remains unknown how the metal-ligand complexes could give rise to such superb mechanical properties. Here, combining single molecule force spectroscopy and quantum calculation, we study the mechanical properties of individual catechol-Fe3 + complexes, the key elements accounting for the high toughness and extensibility of byssal threads of marine mussels. We find that catechol-Fe3 + complexes possess a unique combination of mechanical features, including high mechanical stability, fast reformation kinetics, and stoichiometry-dependent mechanics. Therefore, they can serve as sacrificial bonds to efficiently dissipate energy in the material, quickly recover the mechanical properties when load is released, and be responsive to environmental conditions. Our study provides the mechanistic understanding of the coordination bond-mediated mechanical properties of biogenetic materials, and could guide future rational design and regulation of the mechanical properties of synthetic materials.

  7. Prediction model for aneuploidy in early human embryo development revealed by single-cell analysis

    Science.gov (United States)

    Vera-Rodriguez, Maria; Chavez, Shawn L.; Rubio, Carmen; Pera, Renee A. Reijo; Simon, Carlos

    2015-01-01

    Aneuploidies are prevalent in the human embryo and impair proper development, leading to cell cycle arrest. Recent advances in imaging and molecular and genetic analyses are postulated as promising strategies to unveil the mechanisms involved in aneuploidy generation. Here we combine time-lapse, complete chromosomal assessment and single-cell RT–qPCR to simultaneously obtain information from all cells that compose a human embryo until the approximately eight-cell stage (n=85). Our data indicate that the chromosomal status of aneuploid embryos (n=26), including those that are mosaic (n=3), correlates with significant differences in the duration of the first mitotic phase when compared with euploid embryos (n=28). Moreover, gene expression profiling suggests that a subset of genes is differentially expressed in aneuploid embryos during the first 30 h of development. Thus, we propose that the chromosomal fate of an embryo is likely determined as early as the pronuclear stage and may be predicted by a 12-gene transcriptomic signature. PMID:26151134

  8. Single-molecule RNA observation in vivo reveals dynamics of co-transcriptional splicing

    Science.gov (United States)

    Ferguson, M. L.; Coulon, A.; de Turris, V.; Palangat, M.; Chow, C. C.; Singer, R. H.; Larson, D. R.

    2013-03-01

    The synthesis of pre-mRNA and the splicing of that pre-mRNA to form completed transcripts requires coordination between two large multi-subunit complexes (the transcription elongation complex and the spliceosome). How this coordination occurs in vivo is unknown. Here we report the first experimental observation of transcription and splicing occurring at the same gene in living cells. By utilizing the PP7/MS2 fluorescent RNA reporter system, we can directly observe two distinct regions of the nascent RNA, allowing us to measure the rise and fall time of the intron and exon of a reporter gene stably integrated into a human cell line. The reporter gene consists of a beta globin gene where we have inserted a 24 RNA hairpin cassette into the intron/exon. Upon synthesis, the RNA hairpins are tightly bound by fluorescently-labeled PP7/MS2 bacteriophage coat proteins. After gene induction, a single locus of active transcription in the nucleus shows fluorescence intensity changes characteristic of the synthesis and excision of the intron/exon. Using fluctuation analysis, we determine the elongation rate to be 1.5 kb/min. From the temporal cross correlation function, we determine that splicing of this gene must be co-transcriptional with a splicing time of ~100 seconds before termination and a ~200 second pause at termination. We propose that dual-color RNA imaging may be extended to investigate other mechanisms of transcription, gene regulation, and RNA processing.

  9. Single-cell genomics reveals complex carbohydrate degradation patterns in poribacterial symbionts of marine sponges

    Science.gov (United States)

    Kamke, Janine; Sczyrba, Alexander; Ivanova, Natalia; Schwientek, Patrick; Rinke, Christian; Mavromatis, Kostas; Woyke, Tanja; Hentschel, Ute

    2013-01-01

    Many marine sponges are hosts to dense and phylogenetically diverse microbial communities that are located in the extracellular matrix of the animal. The candidate phylum Poribacteria is a predominant member of the sponge microbiome and its representatives are nearly exclusively found in sponges. Here we used single-cell genomics to obtain comprehensive insights into the metabolic potential of individual poribacterial cells representing three distinct phylogenetic groups within Poribacteria. Genome sizes were up to 5.4 Mbp and genome coverage was as high as 98.5%. Common features of the poribacterial genomes indicated that heterotrophy is likely to be of importance for this bacterial candidate phylum. Carbohydrate-active enzyme database screening and further detailed analysis of carbohydrate metabolism suggested the ability to degrade diverse carbohydrate sources likely originating from seawater and from the host itself. The presence of uronic acid degradation pathways as well as several specific sulfatases provides strong support that Poribacteria degrade glycosaminoglycan chains of proteoglycans, which are important components of the sponge host matrix. Dominant glycoside hydrolase families further suggest degradation of other glycoproteins in the host matrix. We therefore propose that Poribacteria are well adapted to an existence in the sponge extracellular matrix. Poribacteria may be viewed as efficient scavengers and recyclers of a particular suite of carbon compounds that are unique to sponges as microbial ecosystems. PMID:23842652

  10. Single-cell genomics reveals complex carbohydrate degradation patterns in poribacterial symbionts of marine sponges.

    Science.gov (United States)

    Kamke, Janine; Sczyrba, Alexander; Ivanova, Natalia; Schwientek, Patrick; Rinke, Christian; Mavromatis, Kostas; Woyke, Tanja; Hentschel, Ute

    2013-12-01

    Many marine sponges are hosts to dense and phylogenetically diverse microbial communities that are located in the extracellular matrix of the animal. The candidate phylum Poribacteria is a predominant member of the sponge microbiome and its representatives are nearly exclusively found in sponges. Here we used single-cell genomics to obtain comprehensive insights into the metabolic potential of individual poribacterial cells representing three distinct phylogenetic groups within Poribacteria. Genome sizes were up to 5.4 Mbp and genome coverage was as high as 98.5%. Common features of the poribacterial genomes indicated that heterotrophy is likely to be of importance for this bacterial candidate phylum. Carbohydrate-active enzyme database screening and further detailed analysis of carbohydrate metabolism suggested the ability to degrade diverse carbohydrate sources likely originating from seawater and from the host itself. The presence of uronic acid degradation pathways as well as several specific sulfatases provides strong support that Poribacteria degrade glycosaminoglycan chains of proteoglycans, which are important components of the sponge host matrix. Dominant glycoside hydrolase families further suggest degradation of other glycoproteins in the host matrix. We therefore propose that Poribacteria are well adapted to an existence in the sponge extracellular matrix. Poribacteria may be viewed as efficient scavengers and recyclers of a particular suite of carbon compounds that are unique to sponges as microbial ecosystems.

  11. Alternative Spliceosome Assembly Pathways Revealed by Single-Molecule Fluorescence Microscopy

    Directory of Open Access Journals (Sweden)

    Inna Shcherbakova

    2013-10-01

    Full Text Available Removal of introns from nascent transcripts (pre-mRNAs by the spliceosome is an essential step in eukaryotic gene expression. Previous studies have suggested that the earliest steps in spliceosome assembly in yeast are highly ordered and the stable recruitment of U1 small nuclear ribonucleoprotein particle (snRNP to the 5′ splice site necessarily precedes recruitment of U2 snRNP to the branch site to form the “prespliceosome.” Here, using colocalization single-molecule spectroscopy to follow initial spliceosome assembly on eight different S. cerevisiae pre-mRNAs, we demonstrate that active yeast spliceosomes can form by both U1-first and U2-first pathways. Both assembly pathways yield prespliceosomes functionally equivalent for subsequent U5⋅U4/U6 tri-snRNP recruitment and for intron excision. Although fractional flux through the two pathways varies on different introns, both are operational on all introns studied. Thus, multiple pathways exist for assembling functional spliceosomes. These observations provide insight into the mechanisms of cross-intron coordination of initial spliceosome assembly.

  12. Atomic force microscopy reveals two phases in single stranded DNA self-assembled monolayers

    Science.gov (United States)

    Kosaka, Priscila M.; González, Sheila; Domínguez, Carmen M.; Cebollada, Alfonso; San Paulo, Alvaro; Calleja, Montserrat; Tamayo, Javier

    2013-07-01

    We have investigated the structure of single-stranded (ss) DNA self-assembled monolayers (SAMs) on gold by combining peak force tapping, Kelvin probe and phase contrast atomic force microscopy (AFM) techniques. The adhesion, surface potential and phase shift signals show heterogeneities in the DNA film structure at two levels: microscale and nanoscale; which cannot be clearly discerned in the topography. Firstly, there is multilayer aggregation covering less than 5% of the surface. The DNA multilayers seem to be ordered phases and their existence suggests that DNA end-to-end interaction can play a role in the self-assembly process. Secondly, we find the formation of two phases in the DNA monolayer, which differ both in surface energy and surface potential. We relate the two domains to differences in the packing density and in the ssDNA conformation. The discovered heterogeneities in ssDNA SAMs provide a new scenario in our vision of these relevant films that have direct consequences on their biological, chemical and physical properties.

  13. Raman spectroscopy of single extracellular vesicles reveals subpopulations with varying membrane content (Conference Presentation)

    Science.gov (United States)

    Smith, Zachary J.; Lee, Changwon; Rojalin, Tatu; Carney, Randy P.; Hazari, Sidhartha; Knudson, Alisha; Lam, Kit S.; Saari, Heikki; Lazaro Ibañez, Elisa; Viitala, Tapani; Laaksonen, Timo; Yliperttula, Marjo; Wachsmann-Hogiu, Sebastian

    2016-03-01

    Exosomes are small (~100nm) membrane bound vesicles excreted by cells as part of their normal biological processes. These extracellular vesicles are currently an area of intense research, since they were recently found to carry functional mRNA that allows transfer of proteins and other cellular instructions between cells. Exosomes have been implicated in a wide range of diseases, including cancer. Cancer cells are known to have increased exosome production, and may use those exosomes to prepare remote environments for metastasis. Therefore, there is a strong need to develop characterization methods to help understand the structure and function of these vesicles. However, current techniques, such as proteomics and genomics technologies, rely on aggregating a large amount of exosome material and reporting on chemical content that is averaged over many millions of exosomes. Here we report on the use of laser-tweezers Raman spectroscopy (LTRS) to probe individual vesicles, discovering distinct heterogeneity among exosomes both within a cell line, as well as between different cell lines. Through principal components analysis followed by hierarchical clustering, we have identified four "subpopulations" of exosomes shared across seven cell lines. The key chemical differences between these subpopulations, as determined by spectral analysis of the principal component loadings, are primarily related to membrane composition. Specifically, the differences can be ascribed to cholesterol content, cholesterol to phospholipid ratio, and surface protein expression. Thus, we have shown LTRS to be a powerful method to probe the chemical content of single extracellular vesicles.

  14. Structural dynamics of E. coli single-stranded DNA binding protein reveal DNA wrapping and unwrapping pathways.

    Science.gov (United States)

    Suksombat, Sukrit; Khafizov, Rustem; Kozlov, Alexander G; Lohman, Timothy M; Chemla, Yann R

    2015-08-25

    Escherichia coli single-stranded (ss)DNA binding (SSB) protein mediates genome maintenance processes by regulating access to ssDNA. This homotetrameric protein wraps ssDNA in multiple distinct binding modes that may be used selectively in different DNA processes, and whose detailed wrapping topologies remain speculative. Here, we used single-molecule force and fluorescence spectroscopy to investigate E. coli SSB binding to ssDNA. Stretching a single ssDNA-SSB complex reveals discrete states that correlate with known binding modes, the likely ssDNA conformations and diffusion dynamics in each, and the kinetic pathways by which the protein wraps ssDNA and is dissociated. The data allow us to construct an energy landscape for the ssDNA-SSB complex, revealing that unwrapping energy costs increase the more ssDNA is unraveled. Our findings provide insights into the mechanism by which proteins gain access to ssDNA bound by SSB, as demonstrated by experiments in which SSB is displaced by the E. coli recombinase RecA.

  15. Widespread Polycistronic Transcripts in Fungi Revealed by Single-Molecule mRNA Sequencing.

    Directory of Open Access Journals (Sweden)

    Sean P Gordon

    Full Text Available Genes in prokaryotic genomes are often arranged into clusters and co-transcribed into polycistronic RNAs. Isolated examples of polycistronic RNAs were also reported in some higher eukaryotes but their presence was generally considered rare. Here we developed a long-read sequencing strategy to identify polycistronic transcripts in several mushroom forming fungal species including Plicaturopsis crispa, Phanerochaete chrysosporium, Trametes versicolor, and Gloeophyllum trabeum. We found genome-wide prevalence of polycistronic transcription in these Agaricomycetes, involving up to 8% of the transcribed genes. Unlike polycistronic mRNAs in prokaryotes, these co-transcribed genes are also independently transcribed. We show that polycistronic transcription may interfere with expression of the downstream tandem gene. Further comparative genomic analysis indicates that polycistronic transcription is conserved among a wide range of mushroom forming fungi. In summary, our study revealed, for the first time, the genome prevalence of polycistronic transcription in a phylogenetic range of higher fungi. Furthermore, we systematically show that our long-read sequencing approach and combined bioinformatics pipeline is a generic powerful tool for precise characterization of complex transcriptomes that enables identification of mRNA isoforms not recovered via short-read assembly.

  16. Single molecule atomic force microscopy of aerolysin pore complexes reveals unexpected star-shaped topography.

    Science.gov (United States)

    He, Jianfeng; Wang, Jiabin; Hu, Jun; Sun, Jielin; Czajkowsky, Daniel Mark; Shao, Zhifeng

    2016-04-01

    Aerolysin is the paradigmatic member of a large family of toxins that convert from a water-soluble monomer/dimer into a membrane-spanning oligomeric pore. While there is x-ray crystallographic data of its water-soluble conformation, the most recent structural model of the membrane-inserted pore is based primarily on data of water-soluble tetradecamers of mutant protein, together with computational modeling ultimately performed in vacuum. Here we examine this pore model with atomic force microscopy (AFM) of membrane-associated wild-type complexes and all-atom molecular dynamics (MD) simulations in water. In striking contrast to a disc-shaped cap region predicted by the present model, the AFM images reveal a star-shaped complex, with a central ring surrounded by seven radial projections. Further, the MD simulations suggest that the locations of the receptor-binding (D1) domains in the present model are not correct. However, a modified model in which the D1 domains, rather than localized at fixed positions, adopt a wide range of configurations through fluctuations of an intervening linker is compatible with existing data. Thus our work not only demonstrates the importance of directly resolving such complexes in their native environment but also points to a dynamic receptor binding region, which may be critical for toxin assembly on the cell surface.

  17. Development of a PYTHON-based emittance calculator at Fermilab Accelerator Science and Technology (FAST) facility

    Science.gov (United States)

    Green, A. T.

    Beam emittance is an important characteristic describing charged particle beams. In linear accelerators (linac), it is critical to characterize the beam phase space parameters and, in particular, to precisely measure transverse beam emittance. The quadrupole scan (quad-scan) is a well-established technique used to characterize transverse beam parameters in four-dimensional phase space, including beam emittance. A computational algorithm with PYTHON scripts has been developed to estimate beam parameters, in particular beam emittance, using the quad-scan technique in the electron linac at the Fermilab Accelerator Science and Technology (FAST) facility. This script has been implemented in conjunction with an automated quad-scan tool (also written in PYTHON) and has decreased the time it takes to perform a single quad-scan from an hour to a few minutes. From the experimental data, the emittance calculator quickly delivers several results including: geometrical and normalized transverse emittance, Courant-Snyder parameters, and plots of the beam size versus quadrupole field strength, among others. This paper will discuss the details of the techniques used, the results from several quad-scans preformed at FAST during the electron injector commissioning, and the PYTHON code used to obtain the results.

  18. Single cell analysis reveals the stochastic phase of reprogramming to pluripotency is an ordered probabilistic process.

    Directory of Open Access Journals (Sweden)

    Kyung-Min Chung

    Full Text Available Despite years of research, the reprogramming of human somatic cells to pluripotency remains a slow, inefficient process, and a detailed mechanistic understanding of reprogramming remains elusive. Current models suggest reprogramming to pluripotency occurs in two-phases: a prolonged stochastic phase followed by a rapid deterministic phase. In this paradigm, the early stochastic phase is marked by the random and gradual expression of pluripotency genes and is thought to be a major rate-limiting step in the successful generation of induced Pluripotent Stem Cells (iPSCs. Recent evidence suggests that the epigenetic landscape of the somatic cell is gradually reset during a period known as the stochastic phase, but it is known neither how this occurs nor what rate-limiting steps control progress through the stochastic phase. A precise understanding of gene expression dynamics in the stochastic phase is required in order to answer these questions. Moreover, a precise model of this complex process will enable the measurement and mechanistic dissection of treatments that enhance the rate or efficiency of reprogramming to pluripotency. Here we use single-cell transcript profiling, FACS and mathematical modeling to show that the stochastic phase is an ordered probabilistic process with independent gene-specific dynamics. We also show that partially reprogrammed cells infected with OSKM follow two trajectories: a productive trajectory toward increasingly ESC-like expression profiles or an alternative trajectory leading away from both the fibroblast and ESC state. These two pathways are distinguished by the coordinated expression of a small group of chromatin modifiers in the productive trajectory, supporting the notion that chromatin remodeling is essential for successful reprogramming. These are the first results to show that the stochastic phase of reprogramming in human fibroblasts is an ordered, probabilistic process with gene-specific dynamics and to

  19. Single cell analysis reveals the stochastic phase of reprogramming to pluripotency is an ordered probabilistic process.

    Science.gov (United States)

    Chung, Kyung-Min; Kolling, Frederick W; Gajdosik, Matthew D; Burger, Steven; Russell, Alexander C; Nelson, Craig E

    2014-01-01

    Despite years of research, the reprogramming of human somatic cells to pluripotency remains a slow, inefficient process, and a detailed mechanistic understanding of reprogramming remains elusive. Current models suggest reprogramming to pluripotency occurs in two-phases: a prolonged stochastic phase followed by a rapid deterministic phase. In this paradigm, the early stochastic phase is marked by the random and gradual expression of pluripotency genes and is thought to be a major rate-limiting step in the successful generation of induced Pluripotent Stem Cells (iPSCs). Recent evidence suggests that the epigenetic landscape of the somatic cell is gradually reset during a period known as the stochastic phase, but it is known neither how this occurs nor what rate-limiting steps control progress through the stochastic phase. A precise understanding of gene expression dynamics in the stochastic phase is required in order to answer these questions. Moreover, a precise model of this complex process will enable the measurement and mechanistic dissection of treatments that enhance the rate or efficiency of reprogramming to pluripotency. Here we use single-cell transcript profiling, FACS and mathematical modeling to show that the stochastic phase is an ordered probabilistic process with independent gene-specific dynamics. We also show that partially reprogrammed cells infected with OSKM follow two trajectories: a productive trajectory toward increasingly ESC-like expression profiles or an alternative trajectory leading away from both the fibroblast and ESC state. These two pathways are distinguished by the coordinated expression of a small group of chromatin modifiers in the productive trajectory, supporting the notion that chromatin remodeling is essential for successful reprogramming. These are the first results to show that the stochastic phase of reprogramming in human fibroblasts is an ordered, probabilistic process with gene-specific dynamics and to provide a precise

  20. Field emission behavior of carbon nanotube field emitters after high temperature thermal annealing

    Directory of Open Access Journals (Sweden)

    Yuning Sun

    2014-07-01

    Full Text Available The carbon nanotube (CNT field emitters have been fabricated by attaching a CNT film on a graphite rod using graphite adhesive material. The CNT field emitters showed much improved field emission properties due to increasing crystallinity and decreasing defects in CNTs after the high temperature thermal annealing at 900 °C in vacuum ambient. The CNT field emitters showed the low turn-on electric field of 1.15 V/μm, the low threshold electric field of 1.62 V/μm, and the high emission current of 5.9 mA which corresponds to a current density of 8.5 A/cm2. In addition, the CNT field emitters indicated the enhanced field emission properties due to the multi-stage effect when the length of the graphite rod increases. The CNT field emitter showed good field emission stability after the high temperature thermal annealing. The CNT field emitter revealed a focused electron beam spot without any focusing electrodes and also showed good field emission repeatability.

  1. Nonblinking Emitters with Nearly Lifetime-Limited Linewidths in CVD Nanodiamonds

    Science.gov (United States)

    Li, Ke; Zhou, Yu; Rasmita, A.; Aharonovich, I.; Gao, W. B.

    2016-08-01

    Near transform-limited single-photon sources are required for perfect photon indistinguishability in quantum networks. Having such sources in nanodiamonds is particularly important since it can enable engineering hybrid quantum-photonic systems. In this paper, we report the generation of optically stable, nearly transform-limited single silicon-vacancy emitters in nanodiamonds. Lines as narrow as 325 MHz are reported, which is close to the lifetime-limited linewidth (141 MHz). Moreover, the emitters exhibit minimal spectrum diffusion and high photostability, even if pumped well above saturation. Our results suggest that nanodiamonds can host color centers with superior properties suitable for hybrid photonic devices and quantum information.

  2. Non-reciprocal few-photon devices based on chiral waveguide-emitter couplings

    CERN Document Server

    Gonzalez-Ballestero, C; Vidal, F J Garcia; Gonzalez-Tudela, A

    2016-01-01

    We demonstrate the possibility of designing efficient, non reciprocal few-photon devices by exploiting the chiral coupling between two waveguide modes and a single quantum emitter. We show how this system can induce non-reciprocal photon transport at the single-photon level and act as an optical diode. Afterwards, we also show how the same system shows a transistor-like behaviour for a two-photon input. The efficiency in both cases is shown to be large for feasible experimental implementations. Our results illustrate the potential of chiral waveguide-emitter couplings for applications in quantum circuitry.

  3. Single-cell genomics reveals pyrrolysine-encoding potential in members of uncultivated archaeal candidate division MSBL1

    KAUST Repository

    Guan, Yue

    2017-05-11

    Pyrrolysine (Pyl), the 22nd canonical amino acid, is only decoded and synthesized by a limited number of organisms in the domains Archaea and Bacteria. Pyl is encoded by the amber codon UAG, typically a stop codon. To date, all known Pyl-decoding archaea are able to carry out methylotrophic methanogenesis. The functionality of methylamine methyltransferases, an important component of corrinoid-dependent methyltransfer reactions, depends on the presence of Pyl. Here, we present a putative pyl gene cluster obtained from single-cell genomes of the archaeal Mediterranean Sea Brine Lakes group 1 (MSBL1) from the Red Sea. Functional annotation of the MSBL1 single cell amplified genomes (SAGs) also revealed a complete corrinoid-dependent methyl-transfer pathway suggesting that members of MSBL1 may possibly be capable of synthesizing Pyl and metabolizing methylated amines. This article is protected by copyright. All rights reserved.

  4. Early transcriptional and epigenetic regulation of CD8(+) T cell differentiation revealed by single-cell RNA sequencing.

    Science.gov (United States)

    Kakaradov, Boyko; Arsenio, Janilyn; Widjaja, Christella E; He, Zhaoren; Aigner, Stefan; Metz, Patrick J; Yu, Bingfei; Wehrens, Ellen J; Lopez, Justine; Kim, Stephanie H; Zuniga, Elina I; Goldrath, Ananda W; Chang, John T; Yeo, Gene W

    2017-04-01

    During microbial infection, responding CD8(+) T lymphocytes differentiate into heterogeneous subsets that together provide immediate and durable protection. To elucidate the dynamic transcriptional changes that underlie this process, we applied a single-cell RNA-sequencing approach and analyzed individual CD8(+) T lymphocytes sequentially throughout the course of a viral infection in vivo. Our analyses revealed a striking transcriptional divergence among cells that had undergone their first division and identified previously unknown molecular determinants that controlled the fate specification of CD8(+) T lymphocytes. Our findings suggest a model for the differentiation of terminal effector cells initiated by an early burst of transcriptional activity and subsequently refined by epigenetic silencing of transcripts associated with memory lymphocytes, which highlights the power and necessity of single-cell approaches.

  5. Single-molecule imaging reveals topological isomer-dependent diffusion by 4-armed star and dicyclic 8-shaped polymers

    KAUST Repository

    Habuchi, Satoshi

    2015-04-21

    Diffusion dynamics of topological isomers of polymer molecules was investigated at the single-molecule level in a melt state by employing the fluorophore-incorporated 4-armed star and the corresponding doubly-cyclized, 8-shaped poly(THF) chains. While the single-molecule fluorescence imaging experiment revealed that the diffusion of the 4-armed star polymer was described by a single Gaussian distribution, the diffusion of the 8-shaped polymer exhibited a double Gaussian distribution behaviour. We reasoned that the two 8-shaped polymeric isomers have distinct diffusion modes in the melt state, although ensemble-averaged experimental methods cannot detect differences in overall conformational state of the isomers. The single-molecule experiments suggested that one of the 8-shaped polymeric isomer, having the horizontally oriented form, causes an efficient threading with the linear matrix chains which leads to the slower diffusion compared with the corresponding 4-armed star polymer, while the other 8-shaped polymeric isomer, having the vertically oriented form, displayed faster diffusion by the suppression of effective threading with the linear matrix chains due to its contracted chain conformation.

  6. The intrinsic defect structure of exfoliated MoS2 single layers revealed by Scanning Tunneling Microscopy

    Science.gov (United States)

    Vancsó, Péter; Magda, Gábor Zsolt; Pető, János; Noh, Ji-Young; Kim, Yong-Sung; Hwang, Chanyong; Biró, László P.; Tapasztó, Levente

    2016-01-01

    MoS2 single layers have recently emerged as strong competitors of graphene in electronic and optoelectronic device applications due to their intrinsic direct bandgap. However, transport measurements reveal the crucial role of defect-induced electronic states, pointing out the fundamental importance of characterizing their intrinsic defect structure. Transmission Electron Microscopy (TEM) is able to image atomic scale defects in MoS2 single layers, but the imaged defect structure is far from the one probed in the electronic devices, as the defect density and distribution are substantially altered during the TEM imaging. Here, we report that under special imaging conditions, STM measurements can fully resolve the native atomic scale defect structure of MoS2 single layers. Our STM investigations clearly resolve a high intrinsic concentration of individual sulfur atom vacancies, and experimentally identify the nature of the defect induced electronic mid-gap states, by combining topographic STM images with ab intio calculations. Experimental data on the intrinsic defect structure and the associated defect-bound electronic states that can be directly used for the interpretation of transport measurements are essential to fully understand the operation, reliability and performance limitations of realistic electronic devices based on MoS2 single layers. PMID:27445217

  7. Array of chemically etched fused-silica emitters for improving the sensitivity and quantitation of electrospray ionization mass spectrometry.

    Science.gov (United States)

    Kelly, Ryan T; Page, Jason S; Tang, Keqi; Smith, Richard D

    2007-06-01

    An array of emitters has been developed for increasing the sensitivity of electrospray ionization mass spectrometry (ESI-MS). The linear array consists of 19 chemically etched fused-silica capillaries arranged with 500 microm (center-to-center) spacing. The multiemitter device has a low dead volume to facilitate coupling to capillary liquid chromatography (LC) separations. The high aspect ratio of the emitters enables operation at flow rates as low as 20 nL/min/emitter, effectively extending the benefits of nanoelectrospray to higher flow rate analyses. To accommodate the larger ion current produced by the emitter array, a multicapillary inlet to the mass spectrometer was also constructed. The inlet, which matched the dimensions of the emitter array, preserved ion transmission efficiency. Standard reserpine solutions of varying concentration were electrosprayed at 1 microL/min using the multiemitter/multi-inlet combination, and the results were compared to those from a standard, single-emitter configuration. A 9-fold sensitivity enhancement was observed for the multiemitter relative to the single emitter. A bovine serum albumin tryptic digest was also analyzed, and a sensitivity increase ranging from 2.4- to 12.3-fold for the detected tryptic peptides resulted; the varying response was attributed to reduced ion suppression under the nanoESI conditions afforded by the emitter array. An equimolar mixture of leucine enkephalin and maltopentaose was studied to verify that ion suppression is indeed reduced for the multiplexed ESI (multi-ESI) array relative to a single emitter over a range of flow rates.

  8. Applications using high-Tc superconducting terahertz emitters

    Science.gov (United States)

    Nakade, Kurama; Kashiwagi, Takanari; Saiwai, Yoshihiko; Minami, Hidetoshi; Yamamoto, Takashi; Klemm, Richard A.; Kadowaki, Kazuo

    2016-03-01

    Using recently-developed THz emitters constructed from single crystals of the high-Tc superconductor Bi2Sr2CaCu2O8+δ, we performed three prototype tests of the devices to demonstrate their unique characteristic properties for various practical applications. The first is a compact and simple transmission type of THz imaging system using a Stirling cryocooler. The second is a high-resolution Michelson interferometer used as a phase-sensitive reflection-type imaging system. The third is a system with precise temperature control to measure the liquid absorption coefficient. The detailed characteristics of these systems are discussed.

  9. Development of ionic liquid ion source with porous emitter for surface modification

    Energy Technology Data Exchange (ETDEWEB)

    Takeuchi, Mitsuaki, E-mail: m-takeuchi@kuee.kyoto-u.ac.jp; Hamaguchi, Takuya; Ryuto, Hiromichi; Takaoka, Gikan H.

    2013-11-15

    Ionic liquid (IL) ion sources with three different emitter tip materials, stainless steel, tungsten and graphite were developed and examined on ion beam characteristics with respect to its ILs wettability. It was observed that EMIM-BF{sub 4} ion beam produces mostly single cations or anions for positive or negative modes respectively, and exhibits a few cation–anion pairs attached with a cation or an anion. On the other hand, the main content of the BMIM-PF{sub 6} ion beam was the cation–anion pairs while the single ions were minor components. As a result of ion current measurements, the largest and the most stable emission current were obtained for the graphite emitter tip. The results indicate that the emitter wettability plays an important role in the current stability.

  10. Single-Cell Transcript Profiles Reveal Multilineage Priming in Early Progenitors Derived from Lgr5+ Intestinal Stem Cells

    Directory of Open Access Journals (Sweden)

    Tae-Hee Kim

    2016-08-01

    Full Text Available Lgr5+ intestinal stem cells (ISCs drive epithelial self-renewal, and their immediate progeny—intestinal bipotential progenitors—produce absorptive and secretory lineages via lateral inhibition. To define features of early transit from the ISC compartment, we used a microfluidics approach to measure selected stem- and lineage-specific transcripts in single Lgr5+ cells. We identified two distinct cell populations, one that expresses known ISC markers and a second, abundant population that simultaneously expresses markers of stem and mature absorptive and secretory cells. Single-molecule mRNA in situ hybridization and immunofluorescence verified expression of lineage-restricted genes in a subset of Lgr5+ cells in vivo. Transcriptional network analysis revealed that one group of Lgr5+ cells arises from the other and displays characteristics expected of bipotential progenitors, including activation of Notch ligand and cell-cycle-inhibitor genes. These findings define the earliest steps in ISC differentiation and reveal multilineage gene priming as a fundamental property of the process.

  11. Single-Cell Analyses of ESCs Reveal Alternative Pluripotent Cell States and Molecular Mechanisms that Control Self-Renewal

    Directory of Open Access Journals (Sweden)

    Dmitri Papatsenko

    2015-08-01

    Full Text Available Analyses of gene expression in single mouse embryonic stem cells (mESCs cultured in serum and LIF revealed the presence of two distinct cell subpopulations with individual gene expression signatures. Comparisons with published data revealed that cells in the first subpopulation are phenotypically similar to cells isolated from the inner cell mass (ICM. In contrast, cells in the second subpopulation appear to be more mature. Pluripotency Gene Regulatory Network (PGRN reconstruction based on single-cell data and published data suggested antagonistic roles for Oct4 and Nanog in the maintenance of pluripotency states. Integrated analyses of published genomic binding (ChIP data strongly supported this observation. Certain target genes alternatively regulated by OCT4 and NANOG, such as Sall4 and Zscan10, feed back into the top hierarchical regulator Oct4. Analyses of such incoherent feedforward loops with feedback (iFFL-FB suggest a dynamic model for the maintenance of mESC pluripotency and self-renewal.

  12. Visualizing allele-specific expression in single cells reveals epigenetic mosaicism in an H19 loss-of-imprinting mutant.

    Science.gov (United States)

    Ginart, Paul; Kalish, Jennifer M; Jiang, Connie L; Yu, Alice C; Bartolomei, Marisa S; Raj, Arjun

    2016-03-01

    Imprinting is a classic mammalian epigenetic phenomenon that results in expression from a single parental allele. Imprinting defects can lead to inappropriate expression from the normally silenced allele, but it remains unclear whether every cell in a mutant organism follows the population average, which would have profound implications for human imprinting disorders. Here, we apply a new fluorescence in situ hybridization method that measures allele-specific expression in single cells to address this question in mutants exhibiting aberrant H19/Igf2 (insulin-like growth factor 2) imprinting. We show that mutant primary embryonic mouse fibroblasts are comprised of two subpopulations: one expressing both H19 alleles and another expressing only the maternal copy. Only in the latter cell population is Igf2 expression detected. Furthermore, the two subpopulations are stable in that cells do not interconvert between the two expression patterns. Combined small input methylation analysis and transcriptional imaging revealed that these two mutant subpopulations exhibit distinct methylation patterns at their imprinting control regions. Consistently, pharmacological inhibition of DNA methylation reduced the proportion of monoallelic cells. Importantly, we observed that the same two subpopulations are also present in vivo within murine cardiac tissue. Our results establish that imprinting disorders can display striking single-cell heterogeneity in their molecular phenotypes and suggest that such heterogeneity may underlie epigenetic mosaicism in human imprinting disorders.

  13. Package and PCB Effects Shift Intermodulation Notch in an RF Common-Emitter Amplifier

    Directory of Open Access Journals (Sweden)

    J.-M. Wu

    2014-04-01

    Full Text Available A Taylor series analysis is conducted to study the effects of the package and printed circuit board (PCB on the intermodulation nulling of an RF common-emitter amplifier. The equivalent parasitic element of the package and PCB interconnects is extracted from the impedance and admittance parameters, which are obtained using a three-dimensional (3-D electromagnetic simulation tool. The theoretical analysis reveals that the effects of the package and PCB on the intermodulation nulling of common-emitter amplifiers is to shift the intermodulation notch; that the third-order intermodulation (IM3 products under an original bias condition cannot be suppressed and that the linearity of common-emitter amplifiers is thereby degraded. A comparison between theory and simulation reveals good agreement in the predicted locations of the intermodulation notch in the absence and presence of a package and PCB.

  14. A case for ZnO nanowire field emitter arrays in advanced x-ray source applications

    Science.gov (United States)

    Robinson, Vance S.; Bergkvist, Magnus; Chen, Daokun; Chen, Jun; Huang, Mengbing

    2016-09-01

    Reviewing current efforts in X-ray source miniaturization reveals a broad spectrum of applications: Portable and/or remote nondestructive evaluation, high throughput protein crystallography, invasive radiotherapy, monitoring fluid flow and particulate generation in situ, and portable radiography devices for battle-front or large scale disaster triage scenarios. For the most part, all of these applications are being addressed with a top-down approach aimed at improving portability, weight and size. That is, the existing system or a critical sub-component is shrunk in some manner in order to miniaturize the overall package. In parallel to top-down x-ray source miniaturization, more recent efforts leverage field emission and semiconductor device fabrication techniques to achieve small scale x-ray sources via a bottom-up approach where phenomena effective at a micro/nanoscale are coordinated for macro-scale effect. The bottom-up approach holds potential to address all the applications previously mentioned but its entitlement extends into new applications with much more ground-breaking potential. One such bottom-up application is the distributed x-ray source platform. In the medical space, using an array of microscale x-ray sources instead of a single source promises significant reductions in patient dose as well as smaller feature detectability and fewer image artifacts. Cold cathode field emitters are ideal for this application because they can be gated electrostatically or via photonic excitation, they do not generate excessive heat like other common electron emitters, they have higher brightness and they are relatively compact. This document describes how ZnO nanowire field emitter arrays are well suited for distributed x-ray source applications because they hold promise in each of the following critical areas: emission stability, simple scalable fabrication, performance, radiation resistance and photonic coupling.

  15. Modeling of plasmon mediated single-photon devices

    DEFF Research Database (Denmark)

    Chen, Yuntian

    The thesis describes the theoretical study of optical plasmons mediated light-matter interaction. We develop a finite element method to study spontaneous emission from emitters coupled to plasmonic waveguides. The numerical method is applied to calculate the coupling of a emitter coupled to a cyl......-based reconfigurable antenna to controllably distribute emission from a single emitter in spatially separated channels....

  16. High-temperature plasmonic thermal emitter for thermophotovotaics

    DEFF Research Database (Denmark)

    Liu, Jingjing; Guler, Urcan; Li, Wei

    2014-01-01

    We use titanium nitride (TiN) to demonstrate an ultra-thin plasmonic thermal emitter operating at high temperatures (830 K). The spectrally selective emitter exhibits a large emittance at around 2.5 μm and below, and suppresses emission at longer wavelengths.......We use titanium nitride (TiN) to demonstrate an ultra-thin plasmonic thermal emitter operating at high temperatures (830 K). The spectrally selective emitter exhibits a large emittance at around 2.5 μm and below, and suppresses emission at longer wavelengths....

  17. Emittance measurement of high-brightness microbeams

    Energy Technology Data Exchange (ETDEWEB)

    Ishizuka, Hiroshi; Nakahara, Yuriko (Fukuoka Inst. of Tech. (Japan)); Kawasaki, Sunao; Musyoki, S.; Shimizu, Hiroshi; Watanabe, Akihiko; Shiho, Makoto

    1994-09-01

    Arrays of microtriodes have recently become available due to the development of microfabricated field-emission electron sources. Computer simulation has shown that the brightness of beams emitted by them is significantly higher than that of the common microbeams, and possible application of the accelerated beam to free electron lasers has been discussed. Experimentation on beam generation has started, but methods for diagnosing the beam have not yet been established. Difficulty is predicted, because of the high brightness, in applying the conventional methods of emittance measurement. In this paper we propose a new method that determines the emittance without using apertures. The cross section of a converging beam is elongated by a quadrupole lens, and parameters of the emittance ellipse are obtained from the beam size on a screen when changing either the strength or the axial position of the quadrupole lens. (author).

  18. Measurement of transverse emittance and coherence of double-gate field emitter array cathodes

    Science.gov (United States)

    Tsujino, Soichiro; Das Kanungo, Prat; Monshipouri, Mahta; Lee, Chiwon; Miller, R. J. Dwayne

    2016-12-01

    Achieving small transverse beam emittance is important for high brightness cathodes for free electron lasers and electron diffraction and imaging experiments. Double-gate field emitter arrays with on-chip focussing electrode, operating with electrical switching or near infrared laser excitation, have been studied as cathodes that are competitive with photocathodes excited by ultraviolet lasers, but the experimental demonstration of the low emittance has been elusive. Here we demonstrate this for a field emitter array with an optimized double-gate structure by directly measuring the beam characteristics. Further we show the successful application of the double-gate field emitter array to observe the low-energy electron beam diffraction from suspended graphene in minimal setup. The observed low emittance and long coherence length are in good agreement with theory. These results demonstrate that our all-metal double-gate field emitters are highly promising for applications that demand extremely low-electron bunch-phase space volume and large transverse coherence.

  19. In-Plane Electronic Anisotropy of Underdoped ___122___ Fe-Arsenide Superconductors Revealed by Measurements of Detwinned Single Crystals

    Energy Technology Data Exchange (ETDEWEB)

    Fisher, Ian Randal

    2012-05-08

    The parent phases of the Fe-arsenide superconductors harbor an antiferromagnetic ground state. Significantly, the Neel transition is either preceded or accompanied by a structural transition that breaks the four fold symmetry of the high-temperature lattice. Borrowing language from the field of soft condensed matter physics, this broken discrete rotational symmetry is widely referred to as an Ising nematic phase transition. Understanding the origin of this effect is a key component of a complete theoretical description of the occurrence of superconductivity in this family of compounds, motivating both theoretical and experimental investigation of the nematic transition and the associated in-plane anisotropy. Here we review recent experimental progress in determining the intrinsic in-plane electronic anisotropy as revealed by resistivity, reflectivity and ARPES measurements of detwinned single crystals of underdoped Fe arsenide superconductors in the '122' family of compounds.

  20. Visualization of multivalent histone modification in a single cell reveals highly concerted epigenetic changes on differentiation of embryonic stem cells

    DEFF Research Database (Denmark)

    Hattori, Naoko; Niwa, Tohru; Kimura, Kana;

    2013-01-01

    Combinations of histone modifications have significant biological roles, such as maintenance of pluripotency and cancer development, but cannot be analyzed at the single cell level. Here, we visualized a combination of histone modifications by applying the in situ proximity ligation assay, which....... Bivalent modification was clearly visualized by iChmo in wild-type embryonic stem cells (ESCs) known to have it, whereas rarely in Suz12 knockout ESCs and mouse embryonic fibroblasts known to have little of it. iChmo was applied to analysis of epigenetic and phenotypic changes of heterogeneous cell...... population, namely, ESCs at an early stage of differentiation, and this revealed that the bivalent modification disappeared in a highly concerted manner, whereas phenotypic differentiation proceeded with large variations among cells. Also, using this method, we were able to visualize a combination...

  1. Research on Radar Emitter Attribute Recognition Method

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    In order to solve emitter recognition problems in a practical reconnaissance environment, attribute mathematics is introduced. The basic concepts and theory of attribute set and attribute measure are described in detail. A new attribute recognition method based on attribute measure is presented in this paper. Application example is given, which demonstrates this new method is accurate and effective. Moreover, computer simulation for recognizing the emitter purpose is selected, and compared with classical statistical pattern recognition through simulation. The excellent experimental results demonstrate that this is a brand-new attribute recognition method as compared to existing statistical pattern recognition techniques.

  2. Quadrupole Transfer Function for Emittance Measurement

    CERN Document Server

    Cameron, Peter; Jansson, Andreas; Tan, Cheng-Yang

    2008-01-01

    Historically the use of the quadrupole moment measurement has been impeded by the requirement for large dynamic range, as well as measurement sensitivity to beam position. We investigate the use of the transfer function technique [1-3] in combination with the sensitivity and 160dB revolution line rejection of the direct diode detection analog front end [4] to open the possibility of an emittance diagnostic that may be implemented without operational complication, quasi- parasitic to the operation of existing tune measurement systems. Such a diagnostic would be particularly useful as an emittance monitor during acceleration ramp development in machines like RHIC and the LHC.

  3. Current Injection Pumping of Organic Light Emitters

    Science.gov (United States)

    1989-09-28

    MOT-OOO1AF I Current Injection Pumping of Organic Light Emitters Prepared by DI Jeffrey C. Buchholz E L ri: 8 James P. Stec OCT C "t989 Mary C...Schutte Micro -Optics Technologies, Inc. 8608 University Green #5 Middleton, WI 53562 28 September 1989 D,:?UqflON SA2". N’.’ _ Disuibunon Uanu-ted Contract...Title Report Date Current Injection Pumping of Organic Light Emitters 28 September 1989 Authors Jeffrey C. Buchholz, James P. Stec, Mary C. Schutte

  4. Rapid dynamics of general transcription factor TFIIB binding during preinitiation complex assembly revealed by single-molecule analysis

    Science.gov (United States)

    Zhang, Zhengjian; English, Brian P.; Grimm, Jonathan B.; Kazane, Stephanie A.; Hu, Wenxin; Tsai, Albert; Inouye, Carla; You, Changjiang; Piehler, Jacob; Schultz, Peter G.; Lavis, Luke D.; Revyakin, Andrey; Tjian, Robert

    2016-01-01

    Transcription of protein-encoding genes in eukaryotic cells requires the coordinated action of multiple general transcription factors (GTFs) and RNA polymerase II (Pol II). A “step-wise” preinitiation complex (PIC) assembly model has been suggested based on conventional ensemble biochemical measurements, in which protein factors bind stably to the promoter DNA sequentially to build a functional PIC. However, recent dynamic measurements in live cells suggest that transcription factors mostly interact with chromatin DNA rather transiently. To gain a clearer dynamic picture of PIC assembly, we established an integrated in vitro single-molecule transcription platform reconstituted from highly purified human transcription factors and complemented it by live-cell imaging. Here we performed real-time measurements of the hierarchal promoter-specific binding of TFIID, TFIIA, and TFIIB. Surprisingly, we found that while promoter binding of TFIID and TFIIA is stable, promoter binding by TFIIB is highly transient and dynamic (with an average residence time of 1.5 sec). Stable TFIIB–promoter association and progression beyond this apparent PIC assembly checkpoint control occurs only in the presence of Pol II–TFIIF. This transient-to-stable transition of TFIIB-binding dynamics has gone undetected previously and underscores the advantages of single-molecule assays for revealing the dynamic nature of complex biological reactions. PMID:27798851

  5. Single-molecule atomic force microscopy reveals clustering of the yeast plasma-membrane sensor Wsc1.

    Science.gov (United States)

    Heinisch, Jürgen J; Dupres, Vincent; Wilk, Sabrina; Jendretzki, Arne; Dufrêne, Yves F

    2010-06-14

    Signalling is a key feature of living cells which frequently involves the local clustering of specific proteins in the plasma membrane. How such protein clustering is achieved within membrane microdomains ("rafts") is an important, yet largely unsolved problem in cell biology. The plasma membrane of yeast cells represents a good model to address this issue, since it features protein domains that are sufficiently large and stable to be observed by fluorescence microscopy. Here, we demonstrate the ability of single-molecule atomic force microscopy to resolve lateral clustering of the cell integrity sensor Wsc1 in living Saccharomyces cerevisiae cells. We first localize individual wild-type sensors on the cell surface, revealing that they form clusters of approximately 200 nm size. Analyses of three different mutants indicate that the cysteine-rich domain of Wsc1 has a crucial, not yet anticipated function in sensor clustering and signalling. Clustering of Wsc1 is strongly enhanced in deionized water or at elevated temperature, suggesting its relevance in proper stress response. Using in vivo GFP-localization, we also find that non-clustering mutant sensors accumulate in the vacuole, indicating that clustering may prevent endocytosis and sensor turnover. This study represents the first in vivo single-molecule demonstration for clustering of a transmembrane protein in S. cerevisiae. Our findings indicate that in yeast, like in higher eukaryotes, signalling is coupled to the localized enrichment of sensors and receptors within membrane patches.

  6. Single-molecule atomic force microscopy reveals clustering of the yeast plasma-membrane sensor Wsc1.

    Directory of Open Access Journals (Sweden)

    Jürgen J Heinisch

    Full Text Available Signalling is a key feature of living cells which frequently involves the local clustering of specific proteins in the plasma membrane. How such protein clustering is achieved within membrane microdomains ("rafts" is an important, yet largely unsolved problem in cell biology. The plasma membrane of yeast cells represents a good model to address this issue, since it features protein domains that are sufficiently large and stable to be observed by fluorescence microscopy. Here, we demonstrate the ability of single-molecule atomic force microscopy to resolve lateral clustering of the cell integrity sensor Wsc1 in living Saccharomyces cerevisiae cells. We first localize individual wild-type sensors on the cell surface, revealing that they form clusters of approximately 200 nm size. Analyses of three different mutants indicate that the cysteine-rich domain of Wsc1 has a crucial, not yet anticipated function in sensor clustering and signalling. Clustering of Wsc1 is strongly enhanced in deionized water or at elevated temperature, suggesting its relevance in proper stress response. Using in vivo GFP-localization, we also find that non-clustering mutant sensors accumulate in the vacuole, indicating that clustering may prevent endocytosis and sensor turnover. This study represents the first in vivo single-molecule demonstration for clustering of a transmembrane protein in S. cerevisiae. Our findings indicate that in yeast, like in higher eukaryotes, signalling is coupled to the localized enrichment of sensors and receptors within membrane patches.

  7. Single Particle Tracking reveals two distinct environments for CD4 receptors at the surface of living T lymphocytes

    Energy Technology Data Exchange (ETDEWEB)

    Mascalchi, Patrice; Lamort, Anne Sophie; Salome, Laurence [CNRS, IPBS (Institut de Pharmacologie et de Biologie Structurale), 205 route de Narbonne, BP 64182, F-31077 Toulouse (France); Universite de Toulouse, UPS, IPBS (Institut de Pharmacologie et de Biologie Structurale), F-31077 Toulouse (France); Dumas, Fabrice, E-mail: fabrice.dumas@ipbs.fr [CNRS, IPBS (Institut de Pharmacologie et de Biologie Structurale), 205 route de Narbonne, BP 64182, F-31077 Toulouse (France); Universite de Toulouse, UPS, IPBS (Institut de Pharmacologie et de Biologie Structurale), F-31077 Toulouse (France)

    2012-01-06

    Highlights: Black-Right-Pointing-Pointer We studied the diffusion of single CD4 receptors on living lymphocytes. Black-Right-Pointing-Pointer This study reveals that CD4 receptors have either a random or confined diffusion. Black-Right-Pointing-Pointer The dynamics of unconfined CD4 receptors was accelerated by a temperature raise. Black-Right-Pointing-Pointer The dynamics of confined CD4 receptors was unchanged by a temperature raise. Black-Right-Pointing-Pointer Our results suggest the existence of two different environments for CD4 receptors. -- Abstract: We investigated the lateral diffusion of the HIV receptor CD4 at the surface of T lymphocytes at 20 Degree-Sign C and 37 Degree-Sign C by Single Particle Tracking using Quantum Dots. We found that the receptors presented two major distinct behaviors that were not equally affected by temperature changes. About half of the receptors showed a random diffusion with a diffusion coefficient increasing upon raising the temperature. The other half of the receptors was permanently or transiently confined with unchanged dynamics on raising the temperature. These observations suggest that two distinct subpopulations of CD4 receptors with different environments are present at the surface of living T lymphocytes.

  8. Single-virus tracking approach to reveal the interaction of Dengue virus with autophagy during the early stage of infection

    Science.gov (United States)

    Chu, Li-Wei; Huang, Yi-Lung; Lee, Jin-Hui; Huang, Long-Ying; Chen, Wei-Jun; Lin, Ya-Hsuan; Chen, Jyun-Yu; Xiang, Rui; Lee, Chau-Hwang; Ping, Yueh-Hsin

    2014-01-01

    Dengue virus (DENV) is one of the major infectious pathogens worldwide. DENV infection is a highly dynamic process. Currently, no antiviral drug is available for treating DENV-induced diseases since little is known regarding how the virus interacts with host cells during infection. Advanced molecular imaging technologies are powerful tools to understand the dynamics of intracellular interactions and molecular trafficking. This study exploited a single-virus particle tracking technology to address whether DENV interacts with autophagy machinery during the early stage of infection. Using confocal microscopy and three-dimensional image analysis, we showed that DENV triggered the formation of green fluorescence protein-fused microtubule-associated protein 1A/1B-light chain 3 (GFP-LC3) puncta, and DENV-induced autophagosomes engulfed DENV particles within 15-min postinfection. Moreover, single-virus particle tracking revealed that both DENV particles and autophagosomes traveled together during the viral infection. Finally, in the presence of autophagy suppressor 3-methyladenine, the replication of DENV was inhibited and the location of DENV particles spread in cytoplasma. In contrast, the numbers of newly synthesized DENV were elevated and the co-localization of DENV particles and autophagosomes was detected while the cells were treated with autophagy inducer rapamycin. Taken together, we propose that DENV particles interact with autophagosomes at the early stage of viral infection, which promotes the replication of DENV.

  9. Single-cell mass spectrometry reveals small molecules that affect cell fates in the 16-cell embryo.

    Science.gov (United States)

    Onjiko, Rosemary M; Moody, Sally A; Nemes, Peter

    2015-05-26

    Spatial and temporal changes in molecular expression are essential to embryonic development, and their characterization is critical to understand mechanisms by which cells acquire different phenotypes. Although technological advances have made it possible to quantify expression of large molecules during embryogenesis, little information is available on metabolites, the ultimate indicator of physiological activity of the cell. Here, we demonstrate that single-cell capillary electrophoresis-electrospray ionization mass spectrometry is able to test whether differential expression of the genome translates to the domain of metabolites between single embryonic cells. Dissection of three different cell types with distinct tissue fates from 16-cell embryos of the South African clawed frog (Xenopus laevis) and microextraction of their metabolomes enabled the identification of 40 metabolites that anchored interconnected central metabolic networks. Relative quantitation revealed that several metabolites were differentially active between the cell types in the wild-type, unperturbed embryos. Altering postfertilization cytoplasmic movements that perturb dorsal development confirmed that these three cells have characteristic small-molecular activity already at cleavage stages as a result of cell type and not differences in pigmentation, yolk content, cell size, or position in the embryo. Changing the metabolite concentration caused changes in cell movements at gastrulation that also altered the tissue fates of these cells, demonstrating that the metabolome affects cell phenotypes in the embryo.

  10. Differential interaction kinetics of a bipolar structure-specific endonuclease with DNA flaps revealed by single-molecule imaging.

    Directory of Open Access Journals (Sweden)

    Rachid Rezgui

    Full Text Available As DNA repair enzymes are essential for preserving genome integrity, understanding their substrate interaction dynamics and the regulation of their catalytic mechanisms is crucial. Using single-molecule imaging, we investigated the association and dissociation kinetics of the bipolar endonuclease NucS from Pyrococcus abyssi (Pab on 5' and 3'-flap structures under various experimental conditions. We show that association of the PabNucS with ssDNA flaps is largely controlled by diffusion in the NucS-DNA energy landscape and does not require a free 5' or 3' extremity. On the other hand, NucS dissociation is independent of the flap length and thus independent of sliding on the single-stranded portion of the flapped DNA substrates. Our kinetic measurements have revealed previously unnoticed asymmetry in dissociation kinetics from these substrates that is markedly modulated by the replication clamp PCNA. We propose that the replication clamp PCNA enhances the cleavage specificity of NucS proteins by accelerating NucS loading at the ssDNA/dsDNA junctions and by minimizing the nuclease interaction time with its DNA substrate. Our data are also consistent with marked reorganization of ssDNA and nuclease domains occurring during NucS catalysis, and indicate that NucS binds its substrate directly at the ssDNA-dsDNA junction and then threads the ssDNA extremity into the catalytic site. The powerful techniques used here for probing the dynamics of DNA-enzyme binding at the single-molecule have provided new insight regarding substrate specificity of NucS nucleases.

  11. Single-Cell Expression Profiling Reveals a Dynamic State of Cardiac Precursor Cells in the Early Mouse Embryo.

    Directory of Open Access Journals (Sweden)

    Ioannis Kokkinopoulos

    Full Text Available In the early vertebrate embryo, cardiac progenitor/precursor cells (CPs give rise to cardiac structures. Better understanding their biological character is critical to understand the heart development and to apply CPs for the clinical arena. However, our knowledge remains incomplete. With the use of single-cell expression profiling, we have now revealed rapid and dynamic changes in gene expression profiles of the embryonic CPs during the early phase after their segregation from the cardiac mesoderm. Progressively, the nascent mesodermal gene Mesp1 terminated, and Nkx2-5+/Tbx5+ population rapidly replaced the Tbx5low+ population as the expression of the cardiac genes Tbx5 and Nkx2-5 increased. At the Early Headfold stage, Tbx5-expressing CPs gradually showed a unique molecular signature with signs of cardiomyocyte differentiation. Lineage-tracing revealed a developmentally distinct characteristic of this population. They underwent progressive differentiation only towards the cardiomyocyte lineage corresponding to the first heart field rather than being maintained as a progenitor pool. More importantly, Tbx5 likely plays an important role in a transcriptional network to regulate the distinct character of the FHF via a positive feedback loop to activate the robust expression of Tbx5 in CPs. These data expands our knowledge on the behavior of CPs during the early phase of cardiac development, subsequently providing a platform for further study.

  12. One-year survey of a single Micronesian reef reveals extraordinarily rich diversity of Symbiodinium types in soritid foraminifera

    Science.gov (United States)

    Pochon, X.; Garcia-Cuetos, L.; Baker, A. C.; Castella, E.; Pawlowski, J.

    2007-12-01

    Recent molecular studies of symbiotic dinoflagellates (genus Symbiodinium) from a wide array of invertebrate hosts have revealed exceptional fine-scale symbiont diversity whose distribution among hosts, regions and environments exhibits significant biogeographic, ecological and evolutionary patterns. Here, similar molecular approaches using the internal transcribed spacer-2 (ITS-2) region were applied to investigate cryptic diversity in Symbiodinium inhabiting soritid foraminifera. Approximately 1,000 soritid specimens were collected and examined during a 12-month period over a 40 m depth gradient from a single reef in Guam, Micronesia. Out of 61 ITS-2 types distinguished, 46 were novel. Most types found are specific for soritid hosts, except for three types (C1, C15 and C19) that are common in metazoan hosts. The distribution of these symbionts was compared with the phylotype of their foraminiferal hosts, based on soritid small subunit ribosomal DNA sequences, and three new phylotypes of soritid hosts were identified based on these sequences. Phylogenetic analyses of 645 host-symbiont pairings revealed that most Symbiodinium types associated specifically with a particular foraminiferal host genus or species, and that the genetic diversity of these symbiont types was positively correlated with the genetic diversity found within each of the three host genera. Compared to previous molecular studies of Symbiodinium from other locations worldwide, the diversity reported here is exceptional and suggests that Micronesian coral reefs are home to a remarkably large Symbiodinium assemblage.

  13. Brief Report: Single-Cell Analysis Reveals Cell Division-Independent Emergence of Megakaryocytes From Phenotypic Hematopoietic Stem Cells.

    Science.gov (United States)

    Roch, Aline; Trachsel, Vincent; Lutolf, Matthias P

    2015-10-01

    Despite increasingly stringent methods to isolate hematopoietic stem cells (HSCs), considerable heterogeneity remains in terms of their long-term self-renewal and differentiation potential. Recently, the existence of long-lived, self-renewing, myeloid-restricted progenitors in the phenotypically defined HSC compartment has been revealed, but these cells remain poorly characterized. Here, we used an in vitro single-cell analysis approach to track the fate of 330 long-term HSCs (LT-HSC; Lin- cKit+ Sca-1+ CD150+ CD48- CD34-) cultured for 5 days under serum-free basal conditions. Our analysis revealed a highly heterogeneous behavior with approximately 15% of all phenotypic LT-HSCs giving rise to megakaryocytes (Mk). Surprisingly, in 65% of these cases, Mk development occurred in the absence of cell division. This observation suggests that myeloid-restricted progenitors may not derive directly from LT-HSCs but instead could share an identical cell surface marker repertoire. © 2015 AlphaMed Press.

  14. Single-Cell Expression Profiling Reveals a Dynamic State of Cardiac Precursor Cells in the Early Mouse Embryo.

    Science.gov (United States)

    Kokkinopoulos, Ioannis; Ishida, Hidekazu; Saba, Rie; Ruchaya, Prashant; Cabrera, Claudia; Struebig, Monika; Barnes, Michael; Terry, Anna; Kaneko, Masahiro; Shintani, Yasunori; Coppen, Steven; Shiratori, Hidetaka; Ameen, Torath; Mein, Charles; Hamada, Hiroshi; Suzuki, Ken; Yashiro, Kenta

    2015-01-01

    In the early vertebrate embryo, cardiac progenitor/precursor cells (CPs) give rise to cardiac structures. Better understanding their biological character is critical to understand the heart development and to apply CPs for the clinical arena. However, our knowledge remains incomplete. With the use of single-cell expression profiling, we have now revealed rapid and dynamic changes in gene expression profiles of the embryonic CPs during the early phase after their segregation from the cardiac mesoderm. Progressively, the nascent mesodermal gene Mesp1 terminated, and Nkx2-5+/Tbx5+ population rapidly replaced the Tbx5low+ population as the expression of the cardiac genes Tbx5 and Nkx2-5 increased. At the Early Headfold stage, Tbx5-expressing CPs gradually showed a unique molecular signature with signs of cardiomyocyte differentiation. Lineage-tracing revealed a developmentally distinct characteristic of this population. They underwent progressive differentiation only towards the cardiomyocyte lineage corresponding to the first heart field rather than being maintained as a progenitor pool. More importantly, Tbx5 likely plays an important role in a transcriptional network to regulate the distinct character of the FHF via a positive feedback loop to activate the robust expression of Tbx5 in CPs. These data expands our knowledge on the behavior of CPs during the early phase of cardiac development, subsequently providing a platform for further study.

  15. A chip-scale, telecommunications-band frequency conversion interface for quantum emitters.

    Science.gov (United States)

    Agha, Imad; Ates, Serkan; Davanço, Marcelo; Srinivasan, Kartik

    2013-09-09

    We describe a chip-scale, telecommunications-band frequency conversion interface designed for low-noise operation at wavelengths desirable for common single photon emitters. Four-wave-mixing Bragg scattering in silicon nitride waveguides is used to demonstrate frequency upconversion and downconversion between the 980 nm and 1550 nm wavelength regions, with signal-to-background levels > 10 and conversion efficiency of ≈ -60 dB at low continuous wave input pump powers ( 25 % in existing geometries. Finally, we present waveguide designs that can be used to connect shorter wavelength (637 nm to 852 nm) quantum emitters with 1550 nm.

  16. Photon scattering by a three-level emitter in a one-dimensional waveguide

    CERN Document Server

    Witthaut, D

    2010-01-01

    We discuss the scattering of photons from a three-level emitter in a one-dimensional waveguide, where the transport is governed by the interference of spontaneously emitted and directly transmitted waves. The scattering problem is solved in closed form for different level structures. Several possible applications are discussed: The state of the emitter can be switched deterministically by Raman scattering, thus enabling applications in quantum computing such as a single photon transistor. An array of emitters gives rise to a photonic band gap structure, which can be tuned by a classical driving laser. A disordered array leads to Anderson localization of photons, where the localization length can again be controlled by an external driving.

  17. Two-photon interference from independent cavity-coupled emitters on-a-chip

    CERN Document Server

    Kim, Je-Hyung; Leavitt, Richard P; Waks, Edo

    2016-01-01

    Interactions between solid-state quantum emitters and cavities are important for a broad range of applications in quantum communication, linear optical quantum computing, nonlinear photonics, and photonic quantum simulation. These applications often require combining many devices on a single chip with identical emission wavelengths in order to generate two-photon interference, the primary mechanism for achieving effective photon-photon interactions. Such integration remains extremely challenging due to inhomogeneous broadening and fabrication errors that randomize the resonant frequencies of both the emitters and cavities. In this letter we demonstrate two-photon interference from independent cavity-coupled emitters on the same chip, providing a potential solution to this long-standing problem. We overcome spectral mismatch between different cavities due to fabrication errors by depositing and locally evaporating a thin layer of condensed nitrogen. We integrate optical heaters to tune individual dots within e...

  18. Design study of a low-emittance lattice with a five-bend achromat

    Science.gov (United States)

    Liu, Hao-Lin; Kim, Eun-San

    2016-04-01

    The multi-bend achromat (MBA) lattice, which can provide a small horizontal emittance in the subnanometer range, shows promise for future storage-ring-based light-source facilities. We present the linear and the nonlinear properties of an optical design and the results of its optimization. The MBA lattice is designed as a five-bend achromat, and an emittance of 0.270 nm rad is achieved. The energy and the circumference of the designed ring are 3 GeV and 499.3 m, respectively. We investigated an injection system with a single-pulsed sextupole magnet in the storage ring. We describe the space allocation in the injection section and the particle dynamics of the injected beam. The investigation shows that our design exhibits a very low emittance and a sufficient dynamic aperture, and provides a suitable injection scheme for a 3-GeV light source.

  19. Plasmons in doped finite carbon nanotubes and their interactions with fast electrons and quantum emitters

    Science.gov (United States)

    de Vega, Sandra; Cox, Joel D.; de Abajo, F. Javier García

    2016-08-01

    We study the potential of highly doped finite carbon nanotubes to serve as plasmonic elements that mediate the interaction between quantum emitters. Similar to graphene, nanotubes support intense plasmons that can be modulated by varying their level of electrical doping. These excitations exhibit large interaction with light and electron beams, as revealed upon examination of the corresponding light extinction cross-section and electron energy-loss spectra. We show that quantum emitters experience record-high Purcell factors, while they undergo strong mutual interaction mediated by their coupling to the tube plasmons. Our results show the potential of doped finite nanotubes as tunable plasmonic materials for quantum optics applications.

  20. Emittance growth from electron beam modulation

    Energy Technology Data Exchange (ETDEWEB)

    Blaskiewicz, M.

    2009-12-01

    In linac ring colliders like MeRHIC and eRHIC a modulation of the electron bunch can lead to a modulation of the beam beam tune shift and steering errors. These modulations can lead to emittance growth. This note presents simple formulas to estimate these effects which generalize some previous results.

  1. Longitudinal emittance measurements at REX-ISOLDE

    CERN Document Server

    Fraser, M A; Jones, R.M.; Jones, R M; Pasini, M; Posocco, P A; Voulot, D; Wenander, F

    2012-01-01

    We report on measurements of the longitudinal emittance at the Radioactive ion beam EXperiment (REX) at ISOLDE, CERN. The rms longitudinal emittance was measured as 0.34 ± 0.08 π ns keV/u at the output of the RFQ and as 0.36 ± 0.04π ns keV/u in front of the third 7-gap split-ring resonator (7G3) using the three-gradient technique; systematic errors are not included but are estimated at approximately 10%. The 86% emittance was measured a factor of approximately 4.4 times larger than the rms emittance at 1.48 ± 0.2 and 1.55 ± 0.12π ns keV/u at the RFQ and 7G3, respectively. The REX switchyard magnet was used as a spectrometer to analyse the energy spread of the beam as it was manipulated by varying the voltage of the rebuncher (ReB) and 7G3 cavities operating at non-accelerating phases. The transfer matrix for a multi-gap bunching cavity is derived and suitably truncated to allow for the accurate reconstruction of the beam parameters from measurement. The technique for measuring the energy spread was rig...

  2. Highly flexible and robust N-doped SiC nanoneedle field emitters

    KAUST Repository

    Chen, Shanliang

    2015-01-23

    Flexible field emission (FE) emitters, whose unique advantages are lightweight and conformable, promise to enable a wide range of technologies, such as roll-up flexible FE displays, e-papers and flexible light-emitting diodes. In this work, we demonstrate for the first time highly flexible SiC field emitters with low turn-on fields and excellent emission stabilities. n-Type SiC nanoneedles with ultra-sharp tips and tailored N-doping levels were synthesized via a catalyst-assisted pyrolysis process on carbon fabrics by controlling the gas mixture and cooling rate. The turn-on field, threshold field and current emission fluctuation of SiC nanoneedle emitters with an N-doping level of 7.58 at.% are 1.11 V μm-1, 1.55 V μm-1 and 8.1%, respectively, suggesting the best overall performance for such flexible field emitters. Furthermore, characterization of the FE properties under repeated bending cycles and different bending states reveal that the SiC field emitters are mechanically and electrically robust with unprecedentedly high flexibility and stabilities. These findings underscore the importance of concurrent morphology and composition controls in nanomaterial synthesis and establish SiC nanoneedles as the most promising candidate for flexible FE applications. © 2015 Nature Publishing Group All rights reserved.

  3. Beam characterization for the field-emitter-array cathode-based low-emittance gun

    Directory of Open Access Journals (Sweden)

    S. C. Leemann

    2007-07-01

    Full Text Available A 1   Å x-ray free electron laser can be operated at 6 GeV provided a very high brightness electron beam. Therefore, Paul Scherrer Institute has initiated development of the low-emittance gun based on field emission. A field-emitter array (FEA is expected to deliver high peak current while reducing the source emittance to levels close to the thermal limit. A 100 keV gun test stand has been designed in order to gain experience with electron bunches emitted by pulsed FEAs, investigate emittance compensation, and develop diagnostic procedures to characterize the beam. First FEA samples have been installed and pulsed in the gun; the emitted bunches have been accelerated and characterized. We present results acquired with the first FEA samples.

  4. Rare earth boride electron emitter materials fabrication and evaluation

    Science.gov (United States)

    Swanson, L. W.; Davis, P. R.; Gesley, M. A.

    1982-03-01

    Techniques were developed for routine preparation of single crystal rods of LaB6, CeB6 and PrB6 by arc float zone refining. Single crystal, oriented samples were prepared from these rods and mounted as cathodes for testing. Several mounting systems were used, and flat, pointed cone and truncated cone thermionic cathodes were studied. Pointed field emitters of LaB6(100) were also investigated. Variation of thermionic emitted current density and thermal stability of materials were studied as functions of rare earth element, bulk stoichiometry and crystal orientation. Life tests were performed on several different LaB6(100) cathodes. One such cathode operated for over 3000 hours at approximately 10 A/sq cm emitted current density with no serious physical degradation. Surface properties of the materials were investigated by various surface analysis techniques.

  5. What is so super about super-emitters? Characterizing methane high emitters from natural gas infrastructure

    Science.gov (United States)

    Zavala Araiza, D.; Lyon, D. R.; Alvarez, R.; Harriss, R. C.; Palacios, V.; Hamburg, S.

    2015-12-01

    Methane emissions across the natural gas supply chain are dominated at any one time by a few high-emitters (super-emitters or fat-tail of the distribution), often underrepresented in published datasets used to construct emission inventories. Characterization of high-emitters is essential for improving emission estimates based on atmospheric data (top-down) and emission inventories (bottom-up). The population of high-emitters (e.g. 10-20% of sites that account for 80-90% of the emissions) is temporally and spatially dynamic. As a consequence, it is challenging to design sampling methods and construct estimates that accurately represent their frequency and magnitude of emissions. We present new methods to derive facility-specific emission distribution functions that explicitly integrate the influence of the relatively rare super-emitters. These methods were applied in the Barnett Shale region to construct a custom emission inventory that is then compared to top-down emission estimates for the region. We offer a methodological framework relevant to the design of future sampling campaigns, in which these high-emitters are seamlessly incorporated to representative emissions distributions. This framework can be applied to heterogeneous oil and gas production regions across geographies to obtain accurate regional emission estimates. Additionally, we characterize emissions relative to the fraction of a facility's total methane throughput; an effective metric to identify sites with excess emissions resulting from avoidable operating conditions, such as malfunctioning equipment (defined here as functional super-emitters). This work suggests that identifying functional super-emitters and correcting their avoidable operating conditions would result in significant emission reductions. However, due to their spatiotemporal dynamic behavior, achieving and maintaining uniformly low emissions across the entire population of sites will require mitigation steps (e.g. leak detection

  6. Single Enzyme Studies Reveal the Existence of Discrete Functional States for Monomeric Enzymes and How They Are “Selected” upon Allosteric Regulation

    DEFF Research Database (Denmark)

    Hatzakis, Nikos S.; Wei, Li; Jørgensen, Sune Klamer

    2012-01-01

    allosteric regulation of monomeric enzymes is poorly understood. Here we monitored for the first time allosteric regulation of enzymatic activity at the single molecule level. We measured single stochastic catalytic turnovers of a monomeric metabolic enzyme (Thermomyces lanuginosus Lipase) while titrating...... its proximity to a lipid membrane that acts as an allosteric effector. The single molecule measurements revealed the existence of discrete binary functional states that could not be identified in macroscopic measurements due to ensemble averaging. The discrete functional states correlate...

  7. Absorber and emitter for solar thermo-photovoltaic systems to achieve efficiency exceeding the Shockley-Queisser limit.

    Science.gov (United States)

    Rephaeli, Eden; Fan, Shanhui

    2009-08-17

    We present theoretical considerations as well as detailed numerical design of absorber and emitter for Solar Thermophotovoltaics (STPV) applications. The absorber, consisting of an array of tungsten pyramids, was designed to provide near-unity absorptivity over all solar wavelengths for a wide angular range, enabling it to absorb light effectively from solar sources regardless of concentration. The emitter, a tungsten slab with Si/SiO(2) multilayer stack, provides a sharp emissivity peak at the solar cell band-gap while suppressing emission at lower frequencies. We show that, under a suitable light concentration condition, and with a reasonable area ratio between the emitter and absorber, a STPV system employing such absorber-emitter pair and a single-junction solar cell can attain efficiency that exceeds the Shockley-Queisser limit.

  8. Single-particle analysis reveals shutoff control of the Arabidopsis ammonium transporter AMT1;3 by clustering and internalization.

    Science.gov (United States)

    Wang, Qinli; Zhao, Yuanyuan; Luo, Wangxi; Li, Ruili; He, Qihua; Fang, Xiaohong; Michele, Roberto De; Ast, Cindy; von Wirén, Nicolaus; Lin, Jinxing

    2013-08-01

    Ammonium is a preferred source of nitrogen for plants but is toxic at high levels. Plant ammonium transporters (AMTs) play an essential role in NH4(+) uptake, but the mechanism by which AMTs are regulated remains unclear. To study how AMTs are regulated in the presence of ammonium, we used variable-angle total internal reflection fluorescence microscopy and fluorescence cross-correlation spectroscopy for single-particle fluorescence imaging of EGFP-tagged AMT1;3 on the plasma membrane of Arabidopsis root cells at various ammonium levels. We demonstrated that AMT1;3-EGFP dynamically appeared and disappeared on the plasma membrane as moving fluorescent spots in low oligomeric states under N-deprived and N-sufficient conditions. Under external high-ammonium stress, however, AMT1;3-EGFPs were found to amass into clusters, which were then internalized into the cytoplasm. A similar phenomenon also occurred in the glutamine synthetase mutant gln1;2 background. Single-particle analysis of AMT1;3-EGFPs in the clathrin heavy chain 2 mutant (chc2 mutant) and Flotllin1 artificial microRNA (Flot1 amiRNA) backgrounds, together with chemical inhibitor treatments, demonstrated that the endocytosis of AMT1;3 clusters induced by high-ammonium stress could occur mainly through clathrin-mediated endocytic pathways, but the contribution of microdomain-associated endocytic pathway cannot be excluded in the internalization. Our results revealed that the clustering and endocytosis of AMT1;3 provides an effective mechanism by which plant cells can avoid accumulation of toxic levels of ammonium by eliminating active AMT1;3 from the plasma membrane.

  9. Transcriptome sequencing of Eucalyptus camaldulensis seedlings subjected to water stress reveals functional single nucleotide polymorphisms and genes under selection

    Directory of Open Access Journals (Sweden)

    Thumma Bala R

    2012-08-01

    Full Text Available Abstract Background Water stress limits plant survival and production in many parts of the world. Identification of genes and alleles responding to water stress conditions is important in breeding plants better adapted to drought. Currently there are no studies examining the transcriptome wide gene and allelic expression patterns under water stress conditions. We used RNA sequencing (RNA-seq to identify the candidate genes and alleles and to explore the evolutionary signatures of selection. Results We studied the effect of water stress on gene expression in Eucalyptus camaldulensis seedlings derived from three natural populations. We used reference-guided transcriptome mapping to study gene expression. Several genes showed differential expression between control and stress conditions. Gene ontology (GO enrichment tests revealed up-regulation of 140 stress-related gene categories and down-regulation of 35 metabolic and cell wall organisation gene categories. More than 190,000 single nucleotide polymorphisms (SNPs were detected and 2737 of these showed differential allelic expression. Allelic expression of 52% of these variants was correlated with differential gene expression. Signatures of selection patterns were studied by estimating the proportion of nonsynonymous to synonymous substitution rates (Ka/Ks. The average Ka/Ks ratio among the 13,719 genes was 0.39 indicating that most of the genes are under purifying selection. Among the positively selected genes (Ka/Ks > 1.5 apoptosis and cell death categories were enriched. Of the 287 positively selected genes, ninety genes showed differential expression and 27 SNPs from 17 positively selected genes showed differential allelic expression between treatments. Conclusions Correlation of allelic expression of several SNPs with total gene expression indicates that these variants may be the cis-acting variants or in linkage disequilibrium with such variants. Enrichment of apoptosis and cell death gene

  10. Field Emitter Arrays for a Free Electron Laser Application

    CERN Document Server

    Shing-Bruce-Li, Kevin; Ganter, Romain; Gobrecht, Jens; Raguin, Jean Yves; Rivkin, Leonid; Wrulich, Albin F

    2004-01-01

    The development of a new electron gun with the lowest possible emittance would help reducing the total length and cost of a free electron laser. Field emitter arrays (FEAs) are an attractive technology for electron sources of ultra high brightness. Indeed, several thousands of microscopic tips can be deposited on a 1 mm diameter area. Electrons are then extracted by applying voltage to a first grid layer close to the tip apexes, the so called gate layer, and focused by a second grid layer one micrometer above the tips. The typical aperture diameter of the gate and the focusing layer is in the range of one micrometer. One challenge for such cathodes is to produce peak currents in the ampere range since the usual applications of FEAs require less than milliampere. Encouraging peak current performances have been obtained by applying voltage pulses at low frequency between gate and tips. In this paper we report on different tip materials available on the market: diamond FEAs from Extreme Devices Inc., ZrC single ...

  11. Ecology and evolution of viruses infecting uncultivated SUP05 bacteria as revealed by single-cell- and meta-genomics.

    Science.gov (United States)

    Roux, Simon; Hawley, Alyse K; Torres Beltran, Monica; Scofield, Melanie; Schwientek, Patrick; Stepanauskas, Ramunas; Woyke, Tanja; Hallam, Steven J; Sullivan, Matthew B

    2014-08-29

    Viruses modulate microbial communities and alter ecosystem functions. However, due to cultivation bottlenecks, specific virus-host interaction dynamics remain cryptic. In this study, we examined 127 single-cell amplified genomes (SAGs) from uncultivated SUP05 bacteria isolated from a model marine oxygen minimum zone (OMZ) to identify 69 viral contigs representing five new genera within dsDNA Caudovirales and ssDNA Microviridae. Infection frequencies suggest that ∼1/3 of SUP05 bacteria is viral-infected, with higher infection frequency where oxygen-deficiency was most severe. Observed Microviridae clonality suggests recovery of bloom-terminating viruses, while systematic co-infection between dsDNA and ssDNA viruses posits previously unrecognized cooperation modes. Analyses of 186 microbial and viral metagenomes revealed that SUP05 viruses persisted for years, but remained endemic to the OMZ. Finally, identification of virus-encoded dissimilatory sulfite reductase suggests SUP05 viruses reprogram their host's energy metabolism. Together, these results demonstrate closely coupled SUP05 virus-host co-evolutionary dynamics with the potential to modulate biogeochemical cycling in climate-critical and expanding OMZs.

  12. Nanomolar oligomerization and selective co-aggregation of α-synuclein pathogenic mutants revealed by single-molecule fluorescence

    Science.gov (United States)

    Sierecki, Emma; Giles, Nichole; Bowden, Quill; Polinkovsky, Mark E.; Steinbeck, Janina; Arrioti, Nicholas; Rahman, Diya; Bhumkar, Akshay; Nicovich, Philip R.; Ross, Ian; Parton, Robert G.; Böcking, Till; Gambin, Yann

    2016-01-01

    Protein aggregation is a hallmark of many neurodegenerative diseases, notably Alzheimer’s and Parkinson’s disease. Parkinson’s disease is characterized by the presence of Lewy bodies, abnormal aggregates mainly composed of α-synuclein. Moreover, cases of familial Parkinson’s disease have been linked to mutations in α-synuclein. In this study, we compared the behavior of wild-type (WT) α-synuclein and five of its pathological mutants (A30P, E46K, H50Q, G51D and A53T). To this end, single-molecule fluorescence detection was coupled to cell-free protein expression to measure precisely the oligomerization of proteins without purification, denaturation or labelling steps. In these conditions, we could detect the formation of oligomeric and pre-fibrillar species at very short time scale and low micromolar concentrations. The pathogenic mutants surprisingly segregated into two classes: one group forming large aggregates and fibrils while the other tending to form mostly oligomers. Strikingly, co-expression experiments reveal that members from the different groups do not generally interact with each other, both at the fibril and monomer levels. Together, this data paints a completely different picture of α-synuclein aggregation, with two possible pathways leading to the development of fibrils. PMID:27892477

  13. Nanomolar oligomerization and selective co-aggregation of α-synuclein pathogenic mutants revealed by single-molecule fluorescence.

    Science.gov (United States)

    Sierecki, Emma; Giles, Nichole; Bowden, Quill; Polinkovsky, Mark E; Steinbeck, Janina; Arrioti, Nicholas; Rahman, Diya; Bhumkar, Akshay; Nicovich, Philip R; Ross, Ian; Parton, Robert G; Böcking, Till; Gambin, Yann

    2016-11-28

    Protein aggregation is a hallmark of many neurodegenerative diseases, notably Alzheimer's and Parkinson's disease. Parkinson's disease is characterized by the presence of Lewy bodies, abnormal aggregates mainly composed of α-synuclein. Moreover, cases of familial Parkinson's disease have been linked to mutations in α-synuclein. In this study, we compared the behavior of wild-type (WT) α-synuclein and five of its pathological mutants (A30P, E46K, H50Q, G51D and A53T). To this end, single-molecule fluorescence detection was coupled to cell-free protein expression to measure precisely the oligomerization of proteins without purification, denaturation or labelling steps. In these conditions, we could detect the formation of oligomeric and pre-fibrillar species at very short time scale and low micromolar concentrations. The pathogenic mutants surprisingly segregated into two classes: one group forming large aggregates and fibrils while the other tending to form mostly oligomers. Strikingly, co-expression experiments reveal that members from the different groups do not generally interact with each other, both at the fibril and monomer levels. Together, this data paints a completely different picture of α-synuclein aggregation, with two possible pathways leading to the development of fibrils.

  14. Single nucleotide polymorphism typing of Mycobacterium ulcerans reveals focal transmission of buruli ulcer in a highly endemic region of Ghana.

    Directory of Open Access Journals (Sweden)

    Katharina Röltgen

    Full Text Available Buruli ulcer (BU is an emerging necrotizing disease of the skin and subcutaneous tissue caused by Mycobacterium ulcerans. While proximity to stagnant or slow flowing water bodies is a risk factor for acquiring BU, the epidemiology and mode of M. ulcerans transmission is poorly understood. Here we have used high-throughput DNA sequencing and comparisons of the genomes of seven M. ulcerans isolates that appeared monomorphic by existing typing methods. We identified a limited number of single nucleotide polymorphisms (SNPs and developed a real-time PCR SNP typing method based on these differences. We then investigated clinical isolates of M. ulcerans on which we had detailed information concerning patient location and time of diagnosis. Within the Densu river basin of Ghana we observed dominance of one clonal complex and local clustering of some of the variants belonging to this complex. These results reveal focal transmission and demonstrate, that micro-epidemiological analyses by SNP typing has great potential to help us understand how M. ulcerans is transmitted.

  15. DNA methylation profiling at single-base resolution reveals gestational folic acid supplementation influences the epigenome of mouse offspring cerebellum

    Directory of Open Access Journals (Sweden)

    Subit eBarua

    2016-05-01

    Full Text Available It is becoming increasingly more evident that lifestyle, environmental factors, and maternal nutrition during gestation can influence the epigenome of the developing fetus and thus modulate the physiological outcome. Variations in the intake of maternal nutrients affecting one-carbon metabolism may influence brain development and exert long-term effects on the health of the progeny. In this study, we investigated whether supplementation with high maternal folic acid during gestation alters DNA methylation and gene expression in the cerebellum of mouse offspring. We used reduced representation bisulfite sequencing to analyze the DNA methylation profile at the single-base resolution level. The genome-wide DNA methylation analysis revealed that supplementation with higher maternal folic acid resulted in distinct methylation patterns (P < 0.05 of CpG and non-CpG sites in the cerebellum of offspring. Such variations of methylation and gene expression in the cerebellum of offspring were highly sex-specific, including several genes of the neuronal pathways. These findings demonstrate that alterations in the level of maternal folic acid during gestation can influence methylation and gene expression in the cerebellum of offspring. Such changes in the offspring epigenome may alter neurodevelopment and influence the functional outcome of neurologic and psychiatric diseases.

  16. Suppression of the emittance growth induced by CSR in a DBA cell

    CERN Document Server

    Xiao-Hao, Cui; Gang, Xu; Xi-Yang, Huang

    2013-01-01

    The Emittace growth induced by Coherent Synchrotron Radiation(CSR) is an important issue when electron bunches with short bunch length and high peak current are transported in a bending magnet. In this paper, a single kick method is introduced which could give the same result as the R-matrix method, and much easier to use. Then with this method, an optics design technique which could minimize the emittance dilution within a single achromatic cell.

  17. Nanocomposite plasmonic fluorescence emitters with core/shell configurations

    Energy Technology Data Exchange (ETDEWEB)

    Miao, Xiaoyu; Brener, Igal; Luk, Ting Shan

    2010-07-16

    This paper is focused on the optical properties of nanocomposite plasmonic emitters with core/shell configurations, where a fluorescence emitter is located inside a metal nanoshell. Systematic theoretical investigations are presented for the influence of material type, core radius, shell thickness, and excitation wavelength on the internal optical intensity, radiative quantum yield, and fluorescence enhancement of the nanocomposite emitter. It is our conclusion that: (i) an optimal ratio between the core radius and shell thickness is required to maximize the absorption rate of fluorescence emitters, and (ii) a large core radius is desired to minimize the non-radiative damping and avoid significant quantum yield degradation of light emitters. Several experimental approaches to synthesize these nanocomposite emitters are also discussed. Furthermore, our theoretical results are successfully used to explain several reported experimental observations and should prove useful for designing ultra-bright core/shell nanocomposite emitters.

  18. Nanocomposite plasmonic fluorescence emitters with core/shell configurations.

    Energy Technology Data Exchange (ETDEWEB)

    Brener, Igal; Luk, Ting Shan; Miao, Xiaoyu

    2010-06-01

    This paper is focused on the optical properties of nanocomposite plasmonic emitters with core/shell configurations, where a fluorescence emitter is located inside a metal nanoshell. Systematic theoretical investigations are presented for the influence of material type, core radius, shell thickness, and excitation wavelength on the internal optical intensity, radiative quantum yield, and fluorescence enhancement of the nanocomposite emitter. It is our conclusion that: (i) an optimal ratio between the core radius and shell thickness is required to maximize the absorption rate of fluorescence emitters, and (ii) a large core radius is desired to minimize the non-radiative damping and avoid significant quantum yield degradation of light emitters. Several experimental approaches to synthesize these nanocomposite emitters are also discussed. Furthermore, our theoretical results are successfully used to explain several reported experimental observations and should prove useful for designing ultra-bright core/shell nanocomposite emitters.

  19. Emittance growth due to multiple passes through H-minus stripping foil in Booster

    Energy Technology Data Exchange (ETDEWEB)

    Gardner, C. J. [Brookhaven National Lab. (BNL), Upton, NY (United States)

    2017-03-02

    Expressions for transverse emittance growth due to turn-by-turn passes through the H-minus stripping foil in Booster are developed here from simple principles of statistics and simple assumptions about the initial distribution of particles incident on the foil. These are meant to complement work already presented by Zeno [1, 2, 3] and Brown [4]. The expressions show that while the average emittance hEi of the distribution simply increases linearly with turn number, the emittance E based on the mean square particle position does so with an additional oscillatory term that depends on the machine tune. It is shown that this term can be ignored as long as the turn number is su ciently large and the tune is su ciently far from integer and half-integer values. Under these conditions the relation between hEi and E is simply hEi = 2 E. This relation is shown to hold for a Gaussian distribution that is matched to the machine lattice. Two symmetry conditions which help characterize the particle distribution are identi ed. These provide justi cation for calling E an emittance. It is shown that if the conditions are satis ed by the initial distribution, they will not be satis ed after a single traversal of the foil and one turn around the machine. However, on subsequent turns the distribution can (and does) return to satisfying the conditions. Moreover, for su ciently large turn number, the symmetry conditions are approximately satis ed. As already noted in [4], the emittance growth per turn is proportional to the lattice beta at the foil and the mean square angular kick received by protons passing through the foil. We take the former to be 5 m. The latter is obtained from simulations performed with the code TRIM [5]. Having these numbers in hand, actual numbers for emittance growth are presented. The reader may wish to start with Section 11 and refer to previous sections as needed or desired.

  20. Ghost signals in Allison emittance scanners

    Energy Technology Data Exchange (ETDEWEB)

    Stockli, Martin P.; /SNS Project, Oak Ridge /Tennessee U.; Leitner, M.; /LBL, Berkeley; Moehs, D.P.; /Fermilab; Keller, R.; /LBL, Berkeley; Welton, R.F.; /SNS Project, Oak

    2004-12-01

    For over 20 years, Allison scanners have been used to measure emittances of low-energy ion beams. We show that scanning large trajectory angles produces ghost signals caused by the sampled beamlet impacting on an electric deflection plate. The ghost signal strength is proportional to the amount of beam entering the scanner. Depending on the ions, and their velocity, the ghost signals can have the opposite or the same polarity as the main beam signals. The ghost signals cause significant errors in the emittance estimates because they appear at large trajectory angles. These ghost signals often go undetected because they partly overlap with the real signals, are mostly below the 1% level, and often hide in the noise. A simple deflection plate modification is shown to reduce the ghost signal strength by over 99%.

  1. Computing Eigen-Emittances from Tracking Data

    CERN Document Server

    Alexahin, Y

    2014-01-01

    In a strongly nonlinear system the particle distribution in the phase space may develop long tails which contribution to the covariance (sigma) matrix should be suppressed for a correct estimate of the beam emittance. A method is offered based on Gaussian approximation of the original particle distribution in the phase space (Klimontovich distribution) which leads to an equation for the sigma matrix which provides efficient suppression of the tails and cannot be obtained by introducing weights. This equation is easily solved by iterations in the multi-dimensional case. It is also shown how the eigen-emittances and coupled optics functions can be retrieved from the sigma matrix in a strongly coupled system. Finally, the developed algorithm is applied to 6D ionization cooling of muons in HFOFO channel.

  2. An ultracold low emittance electron source

    CERN Document Server

    Xia, G; Murray, A J; Bellan, L; Bertsche, W; Appleby, R B; Mete, O; Chattopadhyay, S

    2014-01-01

    Ultracold atom-based electron sources have recently been proposed as an alternative to the conventional photo-injectors or thermionic electron guns widely used in modern particle accelerators. The advantages of ultracold atom-based electron sources lie in the fact that the electrons extracted from the plasma (created from near threshold photo-ionization of ultracold atoms) have a very low temperature, i.e. down to tens of Kelvin. Extraction of these electrons has the potential for producing very low emittance electron bunches. These features are crucial for the next generation of particle accelerators, including free electron lasers, plasma-based accelerators and future linear colliders. The source also has many potential direct applications, including ultrafast electron diffraction (UED) and electron microscopy, due to its intrinsically high coherence. In this paper, the basic mechanism of ultracold electron beam production is discussed and our new research facility for an ultracold, low emittance electron s...

  3. Computing Eigen-Emittances from Tracking Data

    Energy Technology Data Exchange (ETDEWEB)

    Alexahin, Y. [Fermilab

    2014-09-18

    In a strongly nonlinear system the particle distribution in the phase space may develop long tails which contribution to the covariance (sigma) matrix should be suppressed for a correct estimate of the beam emittance. A method is offered based on Gaussian approximation of the original particle distribution in the phase space (Klimontovich distribution) which leads to an equation for the sigma matrix which provides efficient suppression of the tails and cannot be obtained by introducing weights. This equation is easily solved by iterations in the multi-dimensional case. It is also shown how the eigen-emittances and coupled optics functions can be retrieved from the sigma matrix in a strongly coupled system. Finally, the developed algorithm is applied to 6D ionization cooling of muons in HFOFO channel.

  4. Reverse Emittance Exchange for Muon Colliders

    Energy Technology Data Exchange (ETDEWEB)

    V. Ivanov, A. Afanasev, C.M. Ankenbrandt, R.P. Johnson, G.M. Wang, S.A. Bogacz, Y.S. Derbenev

    2009-05-01

    Muon collider luminosity depends on the number of muons in the storage ring and on the transverse size of the beams in collision. Ionization cooling as it is currently envisioned will not cool the beam sizes sufficiently well to provide adequate luminosity without large muon intensities. Six-dimensional cooling schemes will reduce the longitudinal emittance of a muon beam so that smaller high frequency RF cavities can be used for later stages of cooling and for acceleration. However, the bunch length at collision energy is then shorter than needed to match the interaction region beta function. New ideas to shrink transverse beam dimensions by lengthening each bunch will help achieve high luminosity in muon colliders. Analytic expressions for the reverse emittance exchange mechanism were derived, including a new resonant method of beam focusing.

  5. FIrpic: archetypal blue phosphorescent emitter for electroluminescence.

    Science.gov (United States)

    Baranoff, Etienne; Curchod, Basile F E

    2015-05-14

    FIrpic is the most investigated bis-cyclometallated iridium complex in particular in the context of organic light emitting diodes (OLEDs) because of its attractive sky-blue emission, high emission efficiency, and suitable energy levels. In this Perspective we review the synthesis, structural characterisations, and key properties of this emitter. We also survey the theoretical studies and summarise a series of selected monochromatic electroluminescent devices using FIrpic as the emitting dopant. Finally we highlight important shortcomings of FIrpic as an emitter for OLEDs. Despite the large body of work dedicated to this material, it is manifest that the understanding of photophysical and electrochemical processes are only broadly understood mainly because of the different environment in which these properties are measured, i.e., isolated molecules in solvent vs. device.

  6. Targeted therapy using alpha emitters

    Science.gov (United States)

    Vaidyanathan, Ganesan; Zalutsky, Michael R.

    1996-10-01

    Radionuclides such as and which decay by the emission of -particles are attractive for certain applications of targeted radiotherapy. The tissue penetration of and -particles is equivalent to only a few cell diameters, offering the possibility of combining cell-specific targeting with radiation of similar range. Unlike the -particles emitted by radionuclides such as and , -particles are radiation of high linear energy transfer and thus greater biological effectiveness. Several approaches have been explored for targeted radiotherapy with - and -labelled substances including colloids, monoclonal antibodies, metabolic precursors, receptor-avid ligands and other lower molecular weight molecules. An additional agent which exemplifies the promise of -emitting radiopharmaceuticals is meta-[]astatobenzylguanidine. The toxicity of this compound under single-cell conditions, determined both by []thymidine incorporation and by limiting dilution clonogenic assays, for human neuroblastoma cells is of the order of 1000 times higher than that of meta-[]iodobenzylguanidine. For meta-[]astatobenzylguanidine, the value was equivalent to only atoms bound per cell. These results suggest that meta-[]astatobenzylguanidine might be valuable for the targeted radiotherapy of micrometastatic neuroblastomas.

  7. Single-molecule imaging of DNA pairing by RecA reveals a three-dimensional homology search.

    Science.gov (United States)

    Forget, Anthony L; Kowalczykowski, Stephen C

    2012-02-08

    DNA breaks can be repaired with high fidelity by homologous recombination. A ubiquitous protein that is essential for this DNA template-directed repair is RecA. After resection of broken DNA to produce single-stranded DNA (ssDNA), RecA assembles on this ssDNA into a filament with the unique capacity to search and find DNA sequences in double-stranded DNA (dsDNA) that are homologous to the ssDNA. This homology search is vital to recombinational DNA repair, and results in homologous pairing and exchange of DNA strands. Homologous pairing involves DNA sequence-specific target location by the RecA-ssDNA complex. Despite decades of study, the mechanism of this enigmatic search process remains unknown. RecA is a DNA-dependent ATPase, but ATP hydrolysis is not required for DNA pairing and strand exchange, eliminating active search processes. Using dual optical trapping to manipulate DNA, and single-molecule fluorescence microscopy to image DNA pairing, we demonstrate that both the three-dimensional conformational state of the dsDNA target and the length of the homologous RecA-ssDNA filament have important roles in the homology search. We discovered that as the end-to-end distance of the target dsDNA molecule is increased, constraining the available three-dimensional (3D) conformations of the molecule, the rate of homologous pairing decreases. Conversely, when the length of the ssDNA in the nucleoprotein filament is increased, homology is found faster. We propose a model for the DNA homology search process termed 'intersegmental contact sampling', in which the intrinsic multivalent nature of the RecA nucleoprotein filament is used to search DNA sequence space within 3D domains of DNA, exploiting multiple weak contacts to rapidly search for homology. Our findings highlight the importance of the 3D conformational dynamics of DNA, reveal a previously unknown facet of the homology search, and provide insight into the mechanism of DNA target location by this member of a

  8. Erosion patterns in the Changjiang (Yangtze River) catchment revealed by bulk-sample versus single-mineral provenance budgets

    Science.gov (United States)

    Vezzoli, Giovanni; Garzanti, Eduardo; Limonta, Mara; Andò, Sergio; Yang, Shouye

    2016-05-01

    the East China Sea. Contributions from Tibetan headwaters are negligible, as those from right-bank tributaries in the middle-lower part of the basin. Sediment budgets and erosion patterns inferred from our integrated petrographic and heavy-mineral data set contrast with those based on detrital-zircon geochronology but agree with stream-profile analysis, revealing close correspondence with slope steepness, precipitation, stream power, tectonic activity, and frequency of major earthquakes. Sediment budgets based on amphibole groups are poorly constrained. We conclude that provenance budgets based on single-mineral species are typically unrobust, particularly because they suffer from inaccurate estimates of mineral concentration in the end-member sources. Exploring in detail a millesimal part of the sediment (typically 1/5000 in the case of zircon) is a risky strategy that may return a distorted picture of reality.

  9. Emittance growths in resonance crossing at FFAGs

    Energy Technology Data Exchange (ETDEWEB)

    Ng, K.Y.; /Fermilab; Pang, X.; Wang, F.; Wang, X.; Lee, S.Y.; /Indiana U.

    2007-10-01

    Scaling laws of the emittance growth for a beam crossing the 6th-order systematic space-charge resonances and the random-octupole driven 4th-order resonance are obtained by numerical multi-particle simulations. These laws can be important in setting the minimum acceleration rate and maximum tolerable resonance strength for the design of non-scaling fixed-field alternating gradient accelerators.

  10. Large-area lanthanum hexaboride electron emitter

    Science.gov (United States)

    Goebel, D. M.; Hirooka, Y.; Sketchley, T. A.

    1985-09-01

    The characteristics of lanthanum-boron thermionic electron emitters are discussed, and a large-area, continuously operating cathode assembly and heater are described. Impurity production and structural problems involving the support of the LaB6 have been eliminated in the presented configuration. The performance of the cathode in a plasma discharge, where surface modification occurs by ion sputtering, is presented. Problem areas which affect lifetime and emission current capability are discussed.

  11. Anthropogenic Methane Emissions in California's San Joaquin Valley: Characterizing Large Point Source Emitters

    Science.gov (United States)

    Hopkins, F. M.; Duren, R. M.; Miller, C. E.; Aubrey, A. D.; Falk, M.; Holland, L.; Hook, S. J.; Hulley, G. C.; Johnson, W. R.; Kuai, L.; Kuwayama, T.; Lin, J. C.; Thorpe, A. K.; Worden, J. R.; Lauvaux, T.; Jeong, S.; Fischer, M. L.

    2015-12-01

    Methane is an important atmospheric pollutant that contributes to global warming and tropospheric ozone production. Methane mitigation could reduce near term climate change and improve air quality, but is hindered by a lack of knowledge of anthropogenic methane sources. Recent work has shown that methane emissions are not evenly distributed in space, or across emission sources, suggesting that a large fraction of anthropogenic methane comes from a few "super-emitters." We studied the distribution of super-emitters in California's southern San Joaquin Valley, where elevated levels of atmospheric CH4 have also been observed from space. Here, we define super-emitters as methane plumes that could be reliably detected (i.e., plume observed more than once in the same location) under varying wind conditions by airborne thermal infrared remote sensing. The detection limit for this technique was determined to be 4.5 kg CH4 h-1 by a controlled release experiment, corresponding to column methane enhancement at the point of emissions greater than 20% above local background levels. We surveyed a major oil production field, and an area with a high concentration of large dairies using a variety of airborne and ground-based measurements. Repeated airborne surveys (n=4) with the Hyperspectral Thermal Emission Spectrometer revealed 28 persistent methane plumes emanating from oil field infrastructure, including tanks, wells, and processing facilities. The likelihood that a given source type was a super-emitter varied from roughly 1/3 for processing facilities to 1/3000 for oil wells. 11 persistent plumes were detected in the dairy area, and all were associated with wet manure management. The majority (11/14) of manure lagoons in the study area were super-emitters. Comparing to a California methane emissions inventory for the surveyed areas, we estimate that super-emitters comprise a minimum of 9% of inventoried dairy emissions, and 13% of inventoried oil emissions in this region.

  12. Studying Reionization with Ly-alpha Emitters

    CERN Document Server

    McQuinn, Matthew; Zaldarriaga, Matias; Dutta, Suvendra

    2007-01-01

    We show that observations of high-redshift Ly-alpha emitters (LAEs) have the potential to provide definitive evidence for reionization in the near future. Using 200 Mpc radiative transfer simulations, we calculate the effect that patchy reionization has on the line profile, on the luminosity function, and, most interestingly, on the clustering of emitters for several realistic models of reionization. Reionization increases the measured clustering of emitters, and we show that this enhancement would be essentially impossible to attribute to anything other than reionization. Our results motivate looking for the signature of reionization in existing LAE data. We find that for stellar reionization scenarios the angular correlation function of the 58 LAEs in the Subaru Deep Field z = 6.6 photometric sample is more consistent with a fully ionized universe (mean volume ionized fraction x_i = 1) than a universe with x_i 2-sigma confidence level. Measurements in the next year on Subaru will increase their z = 6.6 LAE ...

  13. The single-giant unilamellar vesicle method reveals lysenin-induced pore formation in lipid membranes containing sphingomyelin.

    Science.gov (United States)

    Alam, Jahangir Md; Kobayashi, Toshihide; Yamazaki, Masahito

    2012-06-26

    Lysenin is a sphingomyelin (SM)-binding pore-forming toxin. To reveal the interaction of lysenin with lipid membranes, we investigated lysenin-induced membrane permeation of a fluorescent probe, calcein, through dioleoylphosphatidylcholine(DOPC)/SM, DOPC/SM/cholesterol(chol), and SM/chol membranes, using the single-giant unilamellar vesicle (GUV) method. The results clearly show that lysenin formed pores in all the membranes, through which membrane permeation of calcein occurred without disruption of GUVs. The membrane permeation began stochastically, and the membrane permeability coefficient increased over time to reach a maximum, steady value, Ps, which persisted for a long time(100--500 s), indicating that the pore concentration increases over time and finally reaches its steady value, NP s . The Ps values increased as the SM/lysenin ratio decreased, and at low concentrations of lysenin, the Ps values of SM/DOPC/chol (42/30/28)GUVs were much larger than those of SM/DOPC (58/42) GUVs. The dependence of Ps on the SM/lysenin ratio for these membranes was almost the same as that of the fraction of sodium dodecyl sulfate (SDS)-resistant lysenin oligomers, indicating that NP s increases as the SDS-resistant oligomer fraction increases. On the other hand, lysenin formed pores in GUVs of SM/chol(60/40) membrane, which is in a homogeneous liquid-ordered phase, indicating that the phase boundary is not necessary for pore formation. The Ps values of SM/chol (60/40) GUVs were smaller than those of SM/DOPC/chol (42/30/28) GUVs even though the SDS-resistant oligomer fractions were similar for both membranes, suggesting that not all of the oligomers can convert into a pore. On the basis of these results, we discuss the elementary processes of lysenin-induced pore formation.

  14. Single-molecule FRET reveals the native-state dynamics of the IκBα ankyrin repeat domain.

    Science.gov (United States)

    Lamboy, Jorge A; Kim, Hajin; Dembinski, Holly; Ha, Taekjip; Komives, Elizabeth A

    2013-07-24

    Previous single-molecule fluorescence resonance energy transfer (smFRET) studies in which the second and sixth ankyrin repeats (ARs) of IκBα were labeled with FRET pairs showed slow fluctuations as if the IκBα AR domain was unfolding in its native state. To systematically probe where these slow dynamic fluctuations occur, we now present data from smFRET studies wherein FRET labels were placed at ARs 1 and 4 (mutant named AR 1-4), at ARs 2 and 5 (AR 2-5), and at ARs 3 and 6 (AR 3-6). The results presented here reveal that AR 6 most readily detaches/unfolds from the AR domain, undergoing substantial fluctuations at room temperature. AR 6 has fewer stabilizing consensus residues than the other IκBα ARs, probably contributing to the ease with which AR 6 "loses grip". AR 5 shows almost no fluctuations at room temperature, but a significant fraction of molecules shows fluctuations at 37 °C. Introduction of stabilizing mutations that are known to fold AR 6 dampen the fluctuations of AR 5, indicating that the AR 5 fluctuations are likely due to weakened inter-repeat stabilization from AR 6. AR 1 also fluctuates somewhat at room temperature, suggesting that fluctuations are a general behavior of ARs at ends of AR domains. Remarkably, AR 1 still fluctuates in the bound state, but mainly between 0.6 and 0.9 FRET efficiency, whereas in the free IκBα, the fluctuations extend to <0.5 FRET efficiency. Overall, our results provide a more complete picture of the energy landscape of the native state dynamics of an AR domain.

  15. Quantum emitters dynamically coupled to a quantum field

    Energy Technology Data Exchange (ETDEWEB)

    Acevedo, O. L.; Quiroga, L.; Rodríguez, F. J. [Departamento de Física, Universidad de los Andes, A.A. 4976, Bogotá (Colombia); Johnson, N. F. [Department of Physics, University of Miami, Coral Gables, Miami, FL 33124 (United States)

    2013-12-04

    We study theoretically the dynamical response of a set of solid-state quantum emitters arbitrarily coupled to a single-mode microcavity system. Ramping the matter-field coupling strength in round trips, we quantify the hysteresis or irreversible quantum dynamics. The matter-field system is modeled as a finite-size Dicke model which has previously been used to describe equilibrium (including quantum phase transition) properties of systems such as quantum dots in a microcavity. Here we extend this model to address non-equilibrium situations. Analyzing the system’s quantum fidelity, we find that the near-adiabatic regime exhibits the richest phenomena, with a strong asymmetry in the internal collective dynamics depending on which phase is chosen as the starting point. We also explore signatures of the crossing of the critical points on the radiation subsystem by monitoring its Wigner function; then, the subsystem can exhibit the emergence of non-classicality and complexity.

  16. Quantum emitters dynamically coupled to a quantum field

    Science.gov (United States)

    Acevedo, O. L.; Quiroga, L.; Rodríguez, F. J.; Johnson, N. F.

    2013-12-01

    We study theoretically the dynamical response of a set of solid-state quantum emitters arbitrarily coupled to a single-mode microcavity system. Ramping the matter-field coupling strength in round trips, we quantify the hysteresis or irreversible quantum dynamics. The matter-field system is modeled as a finite-size Dicke model which has previously been used to describe equilibrium (including quantum phase transition) properties of systems such as quantum dots in a microcavity. Here we extend this model to address non-equilibrium situations. Analyzing the system's quantum fidelity, we find that the near-adiabatic regime exhibits the richest phenomena, with a strong asymmetry in the internal collective dynamics depending on which phase is chosen as the starting point. We also explore signatures of the crossing of the critical points on the radiation subsystem by monitoring its Wigner function; then, the subsystem can exhibit the emergence of non-classicality and complexity.

  17. Emissivity Tuned Emitter for RTPV Power Sources

    Energy Technology Data Exchange (ETDEWEB)

    Carl M. Stoots; Robert C. O' Brien; Troy M. Howe

    2012-03-01

    Every mission launched by NASA to the outer planets has produced unexpected results. The Voyager I and II, Galileo, and Cassini missions produced images and collected scientific data that totally revolutionized our understanding of the solar system and the formation of the planetary systems. These missions were enabled by the use of nuclear power. Because of the distances from the Sun, electrical power was produced using the radioactive decay of a plutonium isotope. Radioisotopic Thermoelectric Generators (RTGs) used in the past and currently used Multi-Mission RTGs (MMRTGs) provide power for space missions. Unfortunately, RTGs rely on thermocouples to convert heat to electricity and are inherently inefficient ({approx} 3-7% thermal to electric efficiency). A Radioisotope Thermal Photovoltaic (RTPV) power source has the potential to reduce the specific mass of the onboard power supply by increasing the efficiency of thermal to electric conversion. In an RTPV, a radioisotope heats an emitter, which emits light to a photovoltaic (PV) cell, which converts the light into electricity. Developing an emitter tuned to the desired wavelength of the photovoltaic is a key part in increasing overall performance. Researchers at the NASA Glenn Research Center (GRC) have built a Thermal Photovoltaic (TPV) system, that utilizes a simulated General Purpose Heat Source (GPHS) from a MMRTG to heat a tantalum emitter. The GPHS is a block of graphite roughly 10 cm by 10 cm by 5 cm. A fully loaded GPHS produces 250 w of thermal power and weighs 1.6 kgs. The GRC system relies on the GPHS unit radiating at 1200 K to a tantalum emitter that, in turn, radiates light to a GaInAs photo-voltaic cell. The GRC claims system efficiency of conversion of 15%. The specific mass is around 167 kg/kWe. A RTPV power source that utilized a ceramic or ceramic-metal (cermet) matrix would allow for the combination of the heat source, canister, and emitter into one compact unit, and allow variation in size

  18. Pulsed laser-deposited nanocrystalline GdB6 thin films on W and Re as field emitters

    Science.gov (United States)

    Suryawanshi, Sachin R.; Singh, Anil K.; Phase, Deodatta M.; Late, Dattatray J.; Sinha, Sucharita; More, Mahendra A.

    2016-10-01

    Gadolinium hexaboride (GdB6) nanocrystalline thin films were grown on tungsten (W), rhenium (Re) tips and foil substrates using optimized pulsed laser deposition (PLD) technique. The X-ray diffraction analysis reveals formation of pure, crystalline cubic phase of GdB6 on W and Re substrates, under the prevailing PLD conditions. The field emission (FE) studies of GdB6/W and GdB6/Re emitters were performed in a planar diode configuration at the base pressure ~10-8 mbar. The GdB6/W and GdB6/Re tip emitters deliver high emission current densities of ~1.4 and 0.811 mA/cm2 at an applied field of ~6.0 and 7.0 V/µm, respectively. The Fowler-Nordheim ( F- N) plots were found to be nearly linear showing metallic nature of the emitters. The noticeably high values of field enhancement factor ( β) estimated using the slopes of the F- N plots indicate that the PLD GdB6 coating on W and Re substrates comprises of high-aspect-ratio nanostructures. Interestingly, the GdB6/W and GdB6/Re planar emitters exhibit excellent current stability at the preset values over a long-term operation, as compared to the tip emitters. Furthermore, the values of workfunction of the GdB6/W and GdB6/Re emitters, experimentally measured using ultraviolet photoelectron spectroscopy, are found to be same, ~1.6 ± 0.1 eV. Despite possessing same workfunction value, the FE characteristics of the GdB6/W emitter are markedly different from that of GdB6/Re emitter, which can be attributed to the growth of GdB6 films on W and Re substrates.

  19. Characterization of single emitters and nano-antennas

    NARCIS (Netherlands)

    Mohtashami, A.

    2015-01-01

    A main promise of the field of physics called "nanophotonics" that deals with nanotechnology to control light, is to provide control over the emission of light sources. Recent developments in the field of solid state lighting that resulted in bright and efficient LEDs, as an example, rely directly u

  20. Strong Coupling of Single Emitters to Surface Plasmons

    Science.gov (United States)

    2007-07-01

    and we find that these two approaches agree closely. In the following, we will consider a nanotip whose sur- face can be parametrized as a paraboloid ...y2 v0 2 − v0 2 , 31 a paraboloid of revolution with apex at z=−v0 2 /2 the reason for the offset of the apex will become apparent below. We now...Eq. 31 is defined by a surface of constant v=v0. More generally, any constant v defines some paraboloid of revolution in this system, while the

  1. Nullspace MUSIC and Improved Radio Frequency Emitter Geolocation from a Mobile Antenna Array

    Science.gov (United States)

    Kintz, Andrew L.

    This work advances state-of-the-art Radio Frequency (RF) emitter geolocation from an airborne or spaceborne antenna array. With an antenna array, geolocation is based on Direction of Arrival (DOA) estimation algorithms such as MUSIC. The MUSIC algorithm applies to arbitrary arrays of polarization sensitive antennas and yields high resolution. However, MUSIC fails to obtain its theoretical resolution for simultaneous, closely spaced, co-frequency signals. We propose the novel Nullspace MUSIC algorithm, which outperforms MUSIC and its existing modifications while maintaining MUSIC(apostrophe)s fundamental orthogonality test. Nullspace MUSIC applies a divide-and-conquer approach and estimates a single DOA at a time. Additionally, an antenna array on an aircraft cannot be perfectly calibrated. RF waves are blocked, reflected, and scattered in a time-varying fashion by the platform around the antenna array. Consequently, full-wave electromagnetics simulations or demanding measurements of the entire platform cannot eliminate the mismatch between the true, in-situ antenna patterns and the antenna patterns that are available for DOA estimation (the antenna array manifold). Platform-induced manifold mismatch severely degrades MUSIC(apostrophe)s resolution and accuracy. We show that Nullspace MUSIC improves DOA accuracy for well separated signals that are incident on an airborne antenna array. Conventionally, geolocation from a mobile platform draws Lines of Bearing (LOB) from the antenna array along the DOAs to find the locations where the DOAs intersect with the ground. However, averaging the LOBs in the global coordinate system yields large errors due to geometric dilution of precision. Since averaging positions fails, a single emitter is typically located by finding the position on the ground that yields the Minimum Apparent Angular Error (MAAE) for the DOA estimates over a flight. We extend the MAAE approach to cluster LOBs from multiple emitters. MAAE clustering

  2. Delay modeling of bipolar ECL/EFL (Emitter-Coupled Logic/Emitter-Follower-Logic) circuits

    Science.gov (United States)

    Yang, Andrew T.

    1986-08-01

    This report deals with the development of a delay-time model for timing simulation of large circuits consisting of Bipolar ECL(Emitter-Coupled Logic) and EFL (Emitter-Follower-Logic) networks. This model can provide adequate information on the performance of the circuits with a minimum expenditure of computation time. This goal is achieved by the use of proper circuit transient models on which analytical delay expressions can be derived with accurate results. The delay-model developed in this report is general enough to handle complex digital circuits with multiple inputs or/and multiple levels. The important effects of input slew rate are also included in the model.

  3. Emittance-dominated long bunches in dual harmonic RF system

    Institute of Scientific and Technical Information of China (English)

    AN Shi-Zhong; Klaus Bongardt; Rudolf Maier; TANG Jing-Yu; ZHANG Tian-Jue

    2008-01-01

    The storage of long bunches for long time intervals needs flattened stationary buckets with a large bucket height. The longitudinal motion of the initially mismatched beam has been studied for both the single and dual harmonic RF systems. The RF amplitude is determined to be r.m.s wise matched. The bucket height of the single harmonic system is too small even for shorter bunch with only 20% increased energy spread. The Halo formation and even debunching can be seen after a few synchrotron periods for single particles with large amplitude. In the case of small energy spread for a cooled beam, Coulomb interaction cannot be ignored. The external voltage has to be increased to keep the r.m.s bunch length unchanged. The new voltage ratio R(N) simplifies physics for the emittance-dominated bunches with modest particle number N. For the single harmonic system, substantial amount of debunching occurs without increasing the external voltage, but very little if the RF amplitude is doubled. Results from the ORBIT tracking code are presented for the 1 GeV bunch in the HESR synchrotron, part of the GSI FAIR project.

  4. High-efficiency fluorescent organic light-emitting diodes enabled by triplet-triplet annihilation and horizontal emitter orientation

    Energy Technology Data Exchange (ETDEWEB)

    Mayr, Christian, E-mail: Christian.Mayr@physik.uni-augsburg.de; Schmidt, Tobias D.; Brütting, Wolfgang, E-mail: Wolfgang.Bruetting@physik.uni-augsburg.de [Institute of Physics, University of Augsburg, 86135 Augsburg (Germany)

    2014-11-03

    A green organic light-emitting diode with the fluorescent emitter Coumarin 545T shows an external quantum efficiency (η{sub EQE}) of 6.9%, clearly exceeding the classical limit of 5% for fluorescent emitters. The analysis of the angular dependent photoluminescence spectrum of the emission layer reveals that 86% of the transition dipole moments are horizontally oriented. Furthermore, transient electroluminescence measurements demonstrate the presence of a delayed emission originating from triplet-triplet annihilation. A simulation based efficiency analysis reveals quantitatively the origin for the high η{sub EQE}: a radiative exciton fraction higher than 25% and a light-outcoupling efficiency of nearly 30%.

  5. Radar Emitter Signal Recognition Based on Complexity Features

    Institute of Scientific and Technical Information of China (English)

    张葛祥; 金炜东; 胡来招

    2004-01-01

    Intra-pulse characteristics of different radar emitter signals reflect on signal waveform by way of changing frequency, phase and amplitude. A novel approach was proposed to extract complexity features of radar emitter signals in a wide range of signal-to-noise ratio ( SNR), and radial basis probability neural network (RBPNN) was used to recognize different radar emitter signals. Complexity features, including Lempel-Ziv complexity (LZC) and correlation dimension (CD), can measure the complexity and irregularity of signals, which mirrors the intra-pulse modulation laws of radar emitter signals. In an experiment, LZC and CD features of 10 typical radar emitter signals were extracted and RBPNN was applied to identify the 10 radar emitter signals. Simulation results show that the proposed approach is effective and has good application values because average accurate recognition rate is high when SNR varies in a wide range.

  6. Fabrication of fiber-optic broadband ultrasound emitters by micro-opto-mechanical technology

    Science.gov (United States)

    Belsito, L.; Vannacci, E.; Mancarella, F.; Ferri, M.; Veronese, G. P.; Biagi, E.; Roncaglia, A.

    2014-08-01

    A micro-opto-mechanical system (MOMS) technology for the fabrication of fiber-optic optoacoustic emitters is presented. The described devices are based on the thermoelastic generation of ultrasonic waves from patterned carbon films obtained by the controlled pyrolysis of photoresist layers and fabricated on miniaturized single-crystal silicon frames used to mount the emitters on the tip of an optical fiber. Thanks to the micromachining process adopted, high miniaturization levels are reached in the fabrication of the emitters, and self-standing devices on optical fiber with diameter around 350 µm are demonstrated, potentially suited to minimally invasive medical applications. The functional testing of fiber-optic emitter prototypes in water performed by using a 1064 nm Q-switched Nd-YAG excitation laser source is also presented, yielding broadband emission spectra extended from low frequencies up to more than 40 MHz, and focused emission fields with a maximum peak-to-peak pressure level of about 1.2 MPa at a distance of 1 mm from the devices.

  7. Nanofabrication of Plasmonic Circuits Containing Single Photon Sources

    DEFF Research Database (Denmark)

    Siampour Ashkavandi, Hamidreza; Kumar, Shailesh; Bozhevolnyi, Sergey I.

    2017-01-01

    -photon emitters, using electron-beam lithography of hydrogen silsesquioxane (HSQ) resist on silver-coated silicon substrates. A propagation length of 20 ± 5 μm for the NV single-photon emission is measured with DLSPPWs. A 5-fold enhancement in the total decay rate, and 58% coupling efficiency to the DLSPPW mode...... is achieved, indicating significant mode confinement. Finally, we demonstrate routing of single plasmons with DLSPPW-based directional couplers, revealing the potential of our approach for on-chip realization of quantum optical networks....

  8. Coated nano-particle jamming of quantum emitters

    DEFF Research Database (Denmark)

    Arslanagic, Samel; Ziolkowski, Richard W.

    2012-01-01

    Spherical active coated nano-particles are examined analytically and numerically in the presence of one, two or four quantum emitters (electric Hertzian dipoles). The ability of the coated nano-particle to effectively cloak the emitters to a far-field observer is reported. This offers an interest...... an interesting route towards the jamming of quantum emitters/nano-antennas, for instance, in biological fluorescence assays....

  9. Thermal emittance measurements of a cesium potassium antimonide photocathode

    Science.gov (United States)

    Bazarov, Ivan; Cultrera, Luca; Bartnik, Adam; Dunham, Bruce; Karkare, Siddharth; Li, Yulin; Liu, Xianghong; Maxson, Jared; Roussel, William

    2011-05-01

    Thermal emittance measurements of a CsK2Sb photocathode at several laser wavelengths are presented. The emittance is obtained with a solenoid scan technique using a high voltage dc photoemission gun. The thermal emittance is 0.56±0.03 mm mrad/mm(rms) at 532 nm wavelength. The results are compared with a simple photoemission model and found to be in a good agreement.

  10. Thermal emittance measurements of a cesium potassium antimonide photocathode

    CERN Document Server

    Bazarov, Ivan; Bartnik, Adam; Dunham, Bruce; Karkare, Siddharth; Li, Yulin; Liu, Xianghong; Maxson, Jared; Roussel, William

    2011-01-01

    Thermal emittance measurements of a CsK2Sb photocathode at several laser wavelengths are presented. The emittance is obtained with a solenoid scan technique using a high voltage dc photoemission gun. The thermal emittance is 0.56+/-0.03 mm-mrad/mm(rms) at 532 nm wavelength. The results are compared with a simple photoemission model and found to be in a good agreement.

  11. Semiconductor Quantum Dash Broadband Emitters: Modeling and Experiments

    KAUST Repository

    Khan, Mohammed Zahed Mustafa

    2013-10-01

    Broadband light emitters operation, which covers multiple wavelengths of the electromagnetic spectrum, has been established as an indispensable element to the human kind, continuously advancing the living standard by serving as sources in important multi-disciplinary field applications such as biomedical imaging and sensing, general lighting and internet and mobile phone connectivity. In general, most commercial broadband light sources relies on complex systems for broadband light generation which are bulky, and energy hungry. \\tRecent demonstration of ultra-broadband emission from semiconductor light sources in the form of superluminescent light emitting diodes (SLDs) has paved way in realization of broadband emitters on a completely novel platform, which offered compactness, cost effectiveness, and comparatively energy efficient, and are already serving as a key component in medical imaging systems. The low power-bandwidth product is inherent in SLDs operating in the amplified spontaneous emission regime. A quantum leap in the advancement of broadband emitters, in which high power and large bandwidth (in tens of nm) are in demand. Recently, the birth of a new class of broadband semiconductor laser diode (LDs) producing multiple wavelength light in stimulated emission regime was demonstrated. This very recent manifestation of a high power-bandwidth-product semiconductor broadband LDs relies on interband optical transitions via quantum confined dot/dash nanostructures and exploiting the natural inhomogeneity of the self-assembled growth technology. This concept is highly interesting and extending the broad spectrum of stimulated emission by novel device design forms the central focus of this dissertation. \\tIn this work, a simple rate equation numerical technique for modeling InAs/InP quantum dash laser incorporating the properties of inhomogeneous broadening effect on lasing spectra was developed and discussed, followed by a comprehensive experimental analysis

  12. Intelligent Variable Emittance Panels Using New, ""True"" Solid Electrolyte Project

    Data.gov (United States)

    National Aeronautics and Space Administration — This work further developed a highly promising Variable Emittance technology for spacecraft thermal control based on Conducting Polymer (CP) electrochromics...

  13. Efficient low-temperature thermophotovoltaic emitters from metallic photonic crystals.

    Science.gov (United States)

    Nagpal, Prashant; Han, Sang Eon; Stein, Andreas; Norris, David J

    2008-10-01

    We examine the use of metallic photonic crystals as thermophotovoltaic emitters. We coat silica woodpile structures, created using direct laser writing, with tungsten or molybdenum. Optical reflectivity and thermal emission measurements near 650 degrees C demonstrate that the resulting structures should provide efficient emitters at relatively low temperatures. When matched to InGaAsSb photocells, our structures should generate over ten times more power than solid emitters while having an optical-to-electrical conversion efficiency above 32%. At such low temperatures, these emitters have promise not only in solar energy but also in harnessing geothermal and industrial waste heat.

  14. Minimum emittance in storage rings with uniform or nonuniform dipoles

    Directory of Open Access Journals (Sweden)

    Chun-xi Wang

    2009-06-01

    Full Text Available A simple treatment of minimum emittance theory in storage rings is presented, favoring vector and matrix forms for a more concise picture. Both conventional uniform dipoles and nonuniform dipoles with bending radius variation are treated. Simple formulas are given for computing the minimum emittance, optimal lattice parameters, as well as effects of nonoptimal parameters. For nonuniform dipoles, analytical results are obtained for a three-piece sandwich dipole model. Minimization of the effective emittance for light sources is given in detail. Usefulness of gradient and/or nonuniform dipoles for reducing the effective emittance is addressed.

  15. LHC MD 652: Coupled-Bunch Instability with Smaller Emittance (all HOMs)

    CERN Document Server

    Esteban Muller, Juan; Timko, Helga; CERN. Geneva. ATS Department

    2017-01-01

    The aim of the MD was to measure the coupled-bunch stability from all HOM impedances, with a reduced longitudinal emittance in order to explore the HL-LHC conditions. The acceleration ramp was performed with the nominal beams of 2016, but a reduced target bunch length and RF voltage. With this reduced emittance, the beam remained close but above the single-bunch stability threshold. No coupled-bunch oscillations were observed, so we can conclude that the stability threshold for coupled-bunch instability is not lower than the single-bunch threshold. An interesting observation in the MD was the long-lasting injection oscillations, whose traces can still be seen at arrival to flat top; in agreement with observations in earlier MDs. The measurements took place between 28th October 20:00 and 29th October 05:10.

  16. Light scattering and photon statistics of quantum emitters coupled to metallic nanoparticles

    Directory of Open Access Journals (Sweden)

    O. Di Stefano

    2011-09-01

    Full Text Available We study theoretically the quantum optical properties of hybrid artificial molecules composed of an individual quantum emitter and a metallic nanoparticle. The coupling between the two systems can give rise to a Fano interference effect which strongly influences the quantum statistical properties of the scattered photons: a small frequency shift of the incident light field may cause changes in the intensity correlation function of the scattered field of orders of magnitude. The system opens a good perspective for applications in active metamaterials and ultracompact single-photon devices. We also demonstrate with accurate scattering calculations that a system constituted by a single quantum emitter (a semiconductor quantum dot placed in the gap between two metallic nanoparticles can display the vacuum Rabi splitting.

  17. High efficiency quasi-monochromatic infrared emitter

    Science.gov (United States)

    Brucoli, Giovanni; Bouchon, Patrick; Haïdar, Riad; Besbes, Mondher; Benisty, Henri; Greffet, Jean-Jacques

    2014-02-01

    Incandescent radiation sources are widely used as mid-infrared emitters owing to the lack of alternative for compact and low cost sources. A drawback of miniature hot systems such as membranes is their low efficiency, e.g., for battery powered systems. For targeted narrow-band applications such as gas spectroscopy, the efficiency is even lower. In this paper, we introduce design rules valid for very generic membranes demonstrating that their energy efficiency for use as incandescent infrared sources can be increased by two orders of magnitude.

  18. Muon Emittance Exchange with a Potato Slicer

    CERN Document Server

    Summers, D J; Acosta, J G; Cremaldi, L M; Oliveros, S J; Perera, L P; Neuffer, D V

    2015-01-01

    We propose a novel scheme for final muon ionization cooling with quadrupole doublets followed by emittance exchange in vacuum to achieve the small beam sizes needed by a muon collider. A flat muon beam with a series of quadrupole doublet half cells appears to provide the strong focusing required for final cooling. Each quadrupole doublet has a low beta region occupied by a dense, low Z absorber. After final cooling, normalized transverse, longitudinal, and angular momentum emittances of 0.100, 2.5, and 0.200 mm-rad are exchanged into 0.025, 70, and 0.0 mm-rad. A skew quadrupole triplet transforms a round muon bunch with modest angular momentum into a flat bunch with no angular momentum. Thin electrostatic septa efficiently slice the flat bunch into 17 parts. The 17 bunches are interleaved into a 3.7 meter long train with RF deflector cavities. Snap bunch coalescence combines the muon bunch train longitudinally in a 21 GeV ring in 55 microseconds, one quarter of a synchrotron oscillation period. A linear long ...

  19. Muon Emittance Exchange with a Potato Slicer

    Energy Technology Data Exchange (ETDEWEB)

    Summers, D. J. [Univ. of Mississippi, Oxford, MS (United States); Hart, T. L. [Univ. of Mississippi, Oxford, MS (United States); Acosta, J. G. [Univ. of Mississippi, Oxford, MS (United States); Cremaldi, L. M. [Univ. of Mississippi, Oxford, MS (United States); Oliveros, S. J. [Univ. of Mississippi, Oxford, MS (United States); Perera, L. P. [Univ. of Mississippi, Oxford, MS (United States); Neuffer, D. V. [Fermi National Accelerator Lab. (FNAL), Batavia, IL (United States)

    2015-04-15

    We propose a novel scheme for final muon ionization cooling with quadrupole doublets followed by emittance exchange in vacuum to achieve the small beam sizes needed by a muon collider. A flat muon beam with a series of quadrupole doublet half cells appears to provide the strong focusing required for final cooling. Each quadrupole doublet has a low beta region occupied by a dense, low Z absorber. After final cooling, normalized transverse, longitudinal, and angular momentum emittances of 0.100, 2.5, and 0.200 mm-rad are exchanged into 0.025, 70, and 0.0 mm-rad. A skew quadrupole triplet transforms a round muon bunch with modest angular momentum into a flat bunch with no angular momentum. Thin electrostatic septa efficiently slice the flat bunch into 17 parts. The 17 bunches are interleaved into a 3.7 meter long train with RF deflector cavities. Snap bunch coalescence combines the muon bunch train longitudinally in a 21 GeV ring in 55 µs, one quarter of a synchrotron oscillation period. A linear long wavelength RF bucket gives each bunch a different energy causing the bunches to drift in the ring until they merge into one bunch and can be captured in a short wavelength RF bucket with a 13% muon decay loss and a packing fraction as high as 87 %.

  20. Therapeutic use of alpha-emitters

    Energy Technology Data Exchange (ETDEWEB)

    Lassmann, M. [Klinik und Poliklinik fuer Nuklearmedizin der Univ. Wuerzburg (Germany)

    2005-07-01

    In recent years there is a growing interest in the therapeutic use of {alpha}-emitters for patient treatment, {alpha}-particles have much higher energy and their range is only a few cell diameters. Their high LET and the limited ability of cells to repair DNA damage from {alpha}-radiation explain their high relative biological effectiveness and cytotoxicity. Potential {alpha}-emitting isotopes for therapeutic applications are {sup 224}Ra, {sup 223}Ra, {sup 213}Bi and {sup 211}At. The treatment with {alpha}-particles is focused upon targeted cancer therapy using radiolabeled monoclonal antibodies, on palliation of bone metastases or upon pain relief in patients with ankylosing spondylitis (AS). Examples for targeted cancer therapy are the treatment of melanoma with {sup 213}Bi and non-Hodgkin lymphoma with {sup 211}At. For metastatic bone pain palliation {sup 223}Ra was applied in a phase I clinical trial. For amelioration of pain in AS-patients {sup 224}Ra-chloride is used. This radiopharmaceutical is licensed for this particular application in Germany. Today there are some potential clinical applications for {alpha}-emitters although most of them are in the state of scientific, non-routine investigations. In-vivo dosimetry for risk assessment associated with this treatment is even more difficult to perform than for therapies using beta-emitting radiopharmaceuticals. (orig.)

  1. Nanoscopic substructures of raft-mimetic liquid-ordered membrane domains revealed by high-speed single-particle tracking

    Science.gov (United States)

    Wu, Hsiao-Mei; Lin, Ying-Hsiu; Yen, Tzu-Chi; Hsieh, Chia-Lung

    2016-02-01

    Lipid rafts are membrane nanodomains that facilitate important cell functions. Despite recent advances in identifying the biological significance of rafts, nature and regulation mechanism of rafts are largely unknown due to the difficulty of resolving dynamic molecular interaction of rafts at the nanoscale. Here, we investigate organization and single-molecule dynamics of rafts by monitoring lateral diffusion of single molecules in raft-containing reconstituted membranes supported on mica substrates. Using high-speed interferometric scattering (iSCAT) optical microscopy and small gold nanoparticles as labels, motion of single lipids is recorded via single-particle tracking (SPT) with nanometer spatial precision and microsecond temporal resolution. Processes of single molecules partitioning into and escaping from the raft-mimetic liquid-ordered (Lo) domains are directly visualized in a continuous manner with unprecedented clarity. Importantly, we observe subdiffusion of saturated lipids in the Lo domain in microsecond timescale, indicating the nanoscopic heterogeneous molecular arrangement of the Lo domain. Further analysis of the diffusion trajectory shows the presence of nano-subdomains of the Lo phase, as small as 10 nm, which transiently trap the lipids. Our results provide the first experimental evidence of non-uniform molecular organization of the Lo phase, giving a new view of how rafts recruit and confine molecules in cell membranes.

  2. Nanoscopic substructures of raft-mimetic liquid-ordered membrane domains revealed by high-speed single-particle tracking.

    Science.gov (United States)

    Wu, Hsiao-Mei; Lin, Ying-Hsiu; Yen, Tzu-Chi; Hsieh, Chia-Lung

    2016-01-01

    Lipid rafts are membrane nanodomains that facilitate important cell functions. Despite recent advances in identifying the biological significance of rafts, nature and regulation mechanism of rafts are largely unknown due to the difficulty of resolving dynamic molecular interaction of rafts at the nanoscale. Here, we investigate organization and single-molecule dynamics of rafts by monitoring lateral diffusion of single molecules in raft-containing reconstituted membranes supported on mica substrates. Using high-speed interferometric scattering (iSCAT) optical microscopy and small gold nanoparticles as labels, motion of single lipids is recorded via single-particle tracking (SPT) with nanometer spatial precision and microsecond temporal resolution. Processes of single molecules partitioning into and escaping from the raft-mimetic liquid-ordered (Lo) domains are directly visualized in a continuous manner with unprecedented clarity. Importantly, we observe subdiffusion of saturated lipids in the Lo domain in microsecond timescale, indicating the nanoscopic heterogeneous molecular arrangement of the Lo domain. Further analysis of the diffusion trajectory shows the presence of nano-subdomains of the Lo phase, as small as 10 nm, which transiently trap the lipids. Our results provide the first experimental evidence of non-uniform molecular organization of the Lo phase, giving a new view of how rafts recruit and confine molecules in cell membranes.

  3. Optimizations of transverse projected emittance at the photo-injector test facility at DESY, location Zeuthen

    Energy Technology Data Exchange (ETDEWEB)

    Rimjaem, S., E-mail: r.sakhorn@gmail.com [Deutsches Elektronen-Synchrotron (DESY), Platanenallee 6, 15738 Zeuthen (Germany); Stephan, F.; Krasilnikov, M. [Deutsches Elektronen-Synchrotron (DESY), Platanenallee 6, 15738 Zeuthen (Germany); Ackermann, W. [Technische Universtaet Darmstadt, Schossgartenstrasse 8, 64289 Darmstadt (Germany); Asova, G.; Baehr, J. [Deutsches Elektronen-Synchrotron (DESY), Platanenallee 6, 15738 Zeuthen (Germany); Gjonaj, E. [Technische Universtaet Darmstadt, Schossgartenstrasse 8, 64289 Darmstadt (Germany); Grabosch, H.J.; Hakobyan, L.; Haenel, M.; Ivanisenko, Y.; Khojoyan, M.; Klemz, G. [Deutsches Elektronen-Synchrotron (DESY), Platanenallee 6, 15738 Zeuthen (Germany); Lederer, S. [Deutsches Elektronen-Synchrotron (DESY), Notkestrasse 85, 22607 Hamburg (Germany); Mahgoub, M. [Deutsches Elektronen-Synchrotron (DESY), Platanenallee 6, 15738 Zeuthen (Germany); Michelato, P.; Monaco, L. [Istituto Nazionale di Fisica Nucleare, Sezione di Milano - LASA, Via F.lli Cervi 201, 20090 Segrate Milano (Italy); Nozdrin, M.; O' Shea, B.; Otevrel, M. [Deutsches Elektronen-Synchrotron (DESY), Platanenallee 6, 15738 Zeuthen (Germany); and others

    2012-04-11

    High brightness electron sources for linac based short-wavelength free-electron lasers are developed and optimized for small transverse projected emittance at the photo-injector test facility at DESY, location Zeuthen (PITZ). A major part of the measurement program at PITZ is dedicated to transverse phase space optimization in order to fulfill the requirements of the European X-ray free-electron laser (European XFEL). A laser-driven RF-gun, treated with a dry-ice sublimation-impulse cleaning technique, a new photocathode laser system allowing short rise and fall times of the flat-top temporal distribution as well as several new diagnostic components have been installed at PITZ in 2008. The electrons generated via the photo-effect at a cesium telluride (Cs{sub 2}Te) cathode are accelerated by a 1.6 cell L-band RF-gun cavity with a maximum accelerating gradient at the cathode of about 60 MV/m. The transverse projected emittance is measured using a single slit scan technique. In the 2008-2009 run period, a detailed characterization of the projected transverse emittance was performed at different operating conditions. Optimizations and measurement results as well as simulation predictions of the transverse projected emittance for bunch charges of 1, 0.5, 0.25 and 0.1 nC are presented and discussed in this paper. The geometric mean of the normalized projected rms emittance in both transverse directions for an electron bunch charge of 1 nC was measured to be 0.89{+-}0.01 mm mrad for a 100% rms phase-space distribution.

  4. Compact Rare Earth Emitter Hollow Cathode

    Science.gov (United States)

    Watkins, Ronald; Goebel, Dan; Hofer, Richard

    2010-01-01

    A compact, high-current, hollow cathode utilizing a lanthanum hexaboride (LaB6) thermionic electron emitter has been developed for use with high-power Hall thrusters and ion thrusters. LaB6 cathodes are being investigated due to their long life, high current capabilities, and less stringent xenon purity and handling requirements compared to conventional barium oxide (BaO) dispenser cathodes. The new cathode features a much smaller diameter than previously developed versions that permit it to be mounted on axis of a Hall thruster ( internally mounted ), as opposed to the conventional side-mount position external to the outer magnetic circuit ("externally mounted"). The cathode has also been reconfigured to be capable of surviving vibrational loads during launch and is designed to solve the significant heater and materials compatibility problems associated with the use of this emitter material. This has been accomplished in a compact design with the capability of high-emission current (10 to 60 A). The compact, high-current design has a keeper diameter that allows the cathode to be mounted on the centerline of a 6- kW Hall thruster, inside the iron core of the inner electromagnetic coil. Although designed for electric propulsion thrusters in spacecraft station- keeping, orbit transfer, and interplanetary applications, the LaB6 cathodes are applicable to the plasma processing industry in applications such as optical coatings and semiconductor processing where reactive gases are used. Where current electrical propulsion thrusters with BaO emitters have limited life and need extremely clean propellant feed systems at a significant cost, these LaB6 cathodes can run on the crudest-grade xenon propellant available without impact. Moreover, in a laboratory environment, LaB6 cathodes reduce testing costs because they do not require extended conditioning periods under hard vacuum. Alternative rare earth emitters, such as cerium hexaboride (CeB6) can be used in this

  5. Intra-Nuclear Single-Particle Tracking (I-SPT) to Reveal the Functional Architecture of Chromosomes.

    Science.gov (United States)

    Récamier, Vincent

    2016-01-01

    Chromosome architecture needs to be investigated in relation with the chemical function of DNA. The kinetics of gene expression, DNA replication, and repair are driven by the mechanisms by which a functional nuclear protein finds its substrate in the nucleus. Single-particle tracking (SPT) is a method to quantify fluorescent molecules dynamics from the tracks of the single molecules recorded by high-resolution microscopes. SPT offers direct observation of the movement and single-molecule resolution. Usually SPT is performed on membranes because of higher contrast. Here, we introduce a novel method to record the trajectories of weakly fluorescent molecules in the nucleus of living cells. I-SPT uses some specific detection and analysis tools to enable the computation of reliable statistics on nuclear particle movement.

  6. Genome-wide divergence and linkage disequilibrium analyses for Capsicum baccatum revealed by genome-anchored single nucleotide polymorphisms

    Science.gov (United States)

    Principal component analysis (PCA) with 36,621 polymorphic genome-anchored single nucleotide polymorphisms (SNPs) identified collectively for Capsicum annuum and Capsicum baccatum was used to show the distribution of these 2 important incompatible cultivated pepper species. Estimated mean nucleotide...

  7. Single-cell expression analyses during cellular reprogramming reveal an early stochastic and a late hierarchic phase

    NARCIS (Netherlands)

    Buganim, Y.; Faddah, D.A.; Cheng, A.W.; Itskovich, E.; Markoulaki, S.; Ganz, K.; Klemm, S.L.; van Oudenaarden, A.; Jaenisch, R.

    2012-01-01

    During cellular reprogramming, only a small fraction of cells become induced pluripotent stem cells (iPSCs). Previous analyses of gene expression during reprogramming were based on populations of cells, impeding single-cell level identification of reprogramming events. We utilized two gene

  8. A single-molecule view of DNA replication : the dynamic nature of multi-protein complexes revealed

    NARCIS (Netherlands)

    Geertsema, Hylkje J.; van Oijen, Antoine M.; Chiu, Wah; Wagner, Gerhard

    2013-01-01

    Recent advances in the development of single-molecule approaches have made it possible to study the dynamics of biomolecular systems in great detail. More recently, such tools have been applied to study the dynamic nature of large multiprotein complexes that support multiple enzymatic activities. In

  9. Single molecule activity measurements of cytochrome P450 oxidoreductase reveal the existence of two discrete functional states

    DEFF Research Database (Denmark)

    Laursen, Tomas; Singha, Aparajita; Rantzau, Nicolai;

    2014-01-01

    Electron transfer between membrane spanning oxidoreductase enzymes controls vital metabolic processes. Here we studied for the first time with single molecule resolution the function of P450 oxidoreductase (POR), the canonical membrane spanning activator of all microsomal cytochrome P450 enzymes....

  10. Genome-wide copy number profiling of single cells in S-phase reveals DNA-replication domains.

    Science.gov (United States)

    Van der Aa, Niels; Cheng, Jiqiu; Mateiu, Ligia; Zamani Esteki, Masoud; Kumar, Parveen; Dimitriadou, Eftychia; Vanneste, Evelyne; Moreau, Yves; Vermeesch, Joris Robert; Voet, Thierry

    2013-04-01

    Single-cell genomics is revolutionizing basic genome research and clinical genetic diagnosis. However, none of the current research or clinical methods for single-cell analysis distinguishes between the analysis of a cell in G1-, S- or G2/M-phase of the cell cycle. Here, we demonstrate by means of array comparative genomic hybridization that charting the DNA copy number landscape of a cell in S-phase requires conceptually different approaches to that of a cell in G1- or G2/M-phase. Remarkably, despite single-cell whole-genome amplification artifacts, the log2 intensity ratios of single S-phase cells oscillate according to early and late replication domains, which in turn leads to the detection of significantly more DNA imbalances when compared with a cell in G1- or G2/M-phase. Although these DNA imbalances may, on the one hand, be falsely interpreted as genuine structural aberrations in the S-phase cell's copy number profile and hence lead to misdiagnosis, on the other hand, the ability to detect replication domains genome wide in one cell has important applications in DNA-replication research. Genome-wide cell-type-specific early and late replicating domains have been identified by analyses of DNA from populations of cells, but cell-to-cell differences in DNA replication may be important in genome stability, disease aetiology and various other cellular processes.

  11. Double hexagonal close-packed structure revealed in a single colloidal crystal grain by Bragg rod analysis

    NARCIS (Netherlands)

    Meijer, J. M.; Shabalin, A.; Dronyak, R.; Yefanov, O. M.; Singer, A.; Kurta, R. P.; Lorenz, U.; Gorobstov, O.; Dzhigaev, D.; Gulden, J.; Byelov, D. V.; Zozulya, A. V.; Sprung, M.; Vartanyants, I. A.; Petukhov, Andrei V.

    2014-01-01

    A coherent X-ray diffraction study of a single colloidal crystal grain composed of silica spheres is reported. The diffraction data contain Bragg peaks and additional features in the form of Bragg rods, which are related to the stacking of the hexagonally close-packed layers. The profile of the Brag

  12. Statistical measurements of quantum emitters coupled to Anderson-localized modes in disordered photonic-crystal waveguides

    NARCIS (Netherlands)

    Javadi, A.; Maibom, S.; Sapienza, L.; Thyrrestrup Nielsen, H.; Garcia, P.D.; Lodahl, P.

    2014-01-01

    We present a statistical study of the Purcell enhancement of the light emission from quantum dots coupled to Anderson-localized cavities formed in disordered photonic-crystal waveguides. We measure the time-resolved light emission from both single quantum emitters coupled to Anderson-localized cavit

  13. Emitter space charge layer transit time in bipolar junction transistors

    Science.gov (United States)

    Rustagi, S. C.; Chattopadhyaya, S. K.

    1981-04-01

    The charge defined emitter space charge layer transit times of double diffused transistors have been calculated using a regional approach, and compared with the corresponding base transit times. The results obtained for emitter space-charge layer transit times have been discussed with reference to the capacitance analysis of Morgan and Smit (1960) for graded p-n junctions.

  14. TOMOGRAPHIC MEASUREMENT OF LONGITUDINAL EMITTANCE GROWTH DUE TO STRIPPING FOILS.

    Energy Technology Data Exchange (ETDEWEB)

    MONTAG, C.; AHRENS, L.; THIEBERGER, P.

    2005-05-16

    During beam acceleration in the Brookhaven accelerator complex, heavy ions are stripped of their electrons in several steps. Depending on the properties of the stripping foils, this process results in an increased energy spread and longitudinal emittance growth. A tomographic phase space reconstruction technique has been applied to measure the associated emittance growth for different stripping foil materials.

  15. Bunch transverse emittance increase in electron storage rings

    Institute of Scientific and Technical Information of China (English)

    GAO Jie

    2009-01-01

    In this paper a theoretical framework to estimate the bunch transverse emittance growing in electron storage rings due to short range transverse wakefield of the machine is established. New equilibrium emittance equations are derived and applied to explain the experimentally obtained results in ATF damping ring. This equation will be useful for linear collider damping ring design.

  16. Electronic Warfare:Issues and Challenges for Emitter Classification

    Directory of Open Access Journals (Sweden)

    Manish Gupta

    2011-04-01

    Full Text Available Electronic warfare (EW is an important capability that provides advantage to defence forces over their adversaries. Defence forces gather tactical intelligence through EW sensors, which provide the means to counter hostile actions of enemy forces. Functions of an EW system is threat detection and the area surveillance so as to determine the identity of surrounding emitters. Emitter classification system identifies possible threats by analysing intercepted signals. Problem of identifying emitters based on its intercepted signal characteristics is a challenging problem in electronic warfare studies. Major issues and challenges for emitter classification such as drifting of emitter parameters due to aging, operational characteristic of an emitter, i.e., same emitter can operate on multiple bands and multiple pulse repetition frequencies (PRFs are highlighted. A novel approach based on some well-known statistical methods, e.g., regression analysis, hypothesis testing, and discriminent analysis is proposed. The effectiveness of the proposed approach has been tested over ELINT (Electronic Intelligence data and illustrated using simulation data. The proposed approach can play a solution for wide variety of problems in emitter classification in electronic warfare studies.Defence Science Journal, 2011, 61(3, pp.228-234, DOI:http://dx.doi.org/10.14429/dsj.61.529

  17. Thermionic scanner pinpoints work function of emitter surfaces

    Science.gov (United States)

    Rasor, N. S.

    1966-01-01

    In the electron tube testing, a thermionic scanner makes accurate spatial resolution measurements of the metallic surface work functions of emitters. The scanner determines the emitter function and its local departures from the mean value on a point-by-point basis for display on an oscilloscope.

  18. Studies of phosphorus Gaussian profile emitter silicon solar cells

    Directory of Open Access Journals (Sweden)

    N. Stem

    2001-01-01

    Full Text Available Considering recent modifications on n-type highly doped silicon parameters, an emitter optimization was made based on one-dimensional models with analytical solutions. In order to get good accuracy, a fifth order approximation has been considered. Two kinds of emitters, homogeneous and non-homogeneous, with phosphorus Gaussian profile emitter solar cells were optimized. According to our results: homogeneous emitter solar cells show their maximum efficiencies (h @ 21.60-21.74%with doping levelsnus = 1x10(19 - 5x10(18 (cm-3 and (1.2-2.0 mum emitter thickness range. Non-homogeneous emitter solar cells provide a slightly higher efficiency (eta = 21.82-21.92%, with Ns = 1x10(20 (cm-3 with 2.0 mum thickness under metal-contacted surface and Ns = 1x10(19 - 5x10(18 (cm-3 with (1.2-2.0 mum thickness range, (sheet resistance range 90-100 W/ under passivated surface. Although non-homogeneous emitter solar cells have a higher efficiency than homogeneous emitter ones, the required technology is more complex and their overall interest for practical applications is questionable.

  19. Efficient room-temperature source of polarized single photons

    Science.gov (United States)

    Lukishova, Svetlana G.; Boyd, Robert W.; Stroud, Carlos R.

    2007-08-07

    An efficient technique for producing deterministically polarized single photons uses liquid-crystal hosts of either monomeric or oligomeric/polymeric form to preferentially align the single emitters for maximum excitation efficiency. Deterministic molecular alignment also provides deterministically polarized output photons; using planar-aligned cholesteric liquid crystal hosts as 1-D photonic-band-gap microcavities tunable to the emitter fluorescence band to increase source efficiency, using liquid crystal technology to prevent emitter bleaching. Emitters comprise soluble dyes, inorganic nanocrystals or trivalent rare-earth chelates.

  20. Initial observations of high-charge, low-emittance electron beams at HIBAF (High Brightness Accelerator FEL)

    Energy Technology Data Exchange (ETDEWEB)

    Lumpkin, A.H.; Feldman, R.B.; Carsten, B.E.; Feldman, D.W.; Sheffield, R.L.; Stein, W.E.; Johnson, W.J.; Thode, L.E.; Bender, S.C.; Busch, G.E.

    1990-01-01

    We report our initial measurements of bright (high-charge, low-emittance) electron beams generated at the Los Alamos High Brightness Accelerator FEL (HIBAF) Facility. Normalized emittance values of less than 50 {pi} mm-mrad for charges ranging from 0.7 to 8.7 nC were obtained for single micropulses at a y-waist and at an energy of 14.7 MeV. These measurements were part of the commissioning campaign on the HIBAF photoelectric injector. Macropulse measurements have also been performed and are compared with PARMELA simulations. 5 refs., 8 figs., 3 tabs.

  1. Superradiance of a subwavelength array of independent classical nonlinear emitters

    CERN Document Server

    Nefedkin, N E; Zyablovsky, A A; Pukhov, A A; Vinogradov, A P; Lisyansky, A A

    2015-01-01

    We suggest a mechanism for the emergence of a superradiance burst in a subwavelength array of nonlinear classical emitters. We assume that the emitters interact via their common field of radiative response and that they may have an arbitrary distribution of initially phases. We show that only if this distribution is not uniform, a non-zero field of radiative response arises leading to a superradiance burst. Although this field cannot synchronize the emitters, it forces fast oscillations of a classical nonlinear emitter to have long-period envelopes. Constructive interference in the envelopes creates a large dipole moment of the array which results in a superradiance pulse. The intensity of the superradiance is proportional to the squared number of the emitters, which envelopes participate in the fluctuation.

  2. Properties of nanolasers based on few discrete emitters

    DEFF Research Database (Denmark)

    Lund, Anders Mølbjerg; Nielsen, Per Kær; Lorke, Michael

    2012-01-01

    to a high-Q optical cavity. This system has previously been studied for the one and two emitters case, see e.g. [1, 2]. The emitters and cavity are modelled as two-level systems and a harmonic oscillator, respectively. The coupled system is modelled using the Jaynes-Cummings Hamiltonian and the two......-level systems are pumped incoherently by a rate P. Solutions are found using the corresponding master equation. However, with cavity populations exceeding 100 and several emitters, the dimension of the Hilbert space of the system becomes too large to handle efficiently on a conventional computer. E.g. for four...... emitters and 100 photon states the density matrix has more than 2.5 × 106 elements. We have been able to simplify the problem significantly by adiabatically eliminating the photon-assisted polarizations and the correlations between emitters and cavity [3]. This results in a set of rate equations...

  3. Evaluations of carbon nanotube field emitters for electron microscopy

    Science.gov (United States)

    Nakahara, Hitoshi; Kusano, Yoshikazu; Kono, Takumi; Saito, Yahachi

    2009-11-01

    Brightness of carbon nanotube (CNT) emitters was already reported elsewhere. However, brightness of electron emitter is affected by a virtual source size of the emitter, which strongly depends on electron optical configuration around the emitter. In this work, I- V characteristics and brightness of a CNT emitter are measured under a practical field emission electron gun (e-gun) configuration to investigate availability of CNT for electron microscopy. As a result, it is obtained that an emission area of MWNT is smaller than its tip surface area, and the emission area corresponds to a five-membered-ring with 2nd nearest six-membered-rings on the MWNT cap surface. Reduced brightness of MWNT is measured as at least 2.6×109 A/m 2 sr V. It is concluded that even a thick MWNT has enough brightness under a practical e-gun electrode configuration and suitable for electron microscopy.

  4. Evaluations of carbon nanotube field emitters for electron microscopy

    Energy Technology Data Exchange (ETDEWEB)

    Nakahara, Hitoshi, E-mail: nakahara@nagoya-u.jp [Department of Quantum Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603 (Japan); Kusano, Yoshikazu; Kono, Takumi; Saito, Yahachi [Department of Quantum Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603 (Japan)

    2009-11-30

    Brightness of carbon nanotube (CNT) emitters was already reported elsewhere. However, brightness of electron emitter is affected by a virtual source size of the emitter, which strongly depends on electron optical configuration around the emitter. In this work, I-V characteristics and brightness of a CNT emitter are measured under a practical field emission electron gun (e-gun) configuration to investigate availability of CNT for electron microscopy. As a result, it is obtained that an emission area of MWNT is smaller than its tip surface area, and the emission area corresponds to a five-membered-ring with 2nd nearest six-membered-rings on the MWNT cap surface. Reduced brightness of MWNT is measured as at least 2.6x10{sup 9} A/m{sup 2} sr V. It is concluded that even a thick MWNT has enough brightness under a practical e-gun electrode configuration and suitable for electron microscopy.

  5. Ultrashort single-wall carbon nanotubes reveal field-emission coulomb blockade and highest electron-source brightness.

    Science.gov (United States)

    Pascale-Hamri, A; Perisanu, S; Derouet, A; Journet, C; Vincent, P; Ayari, A; Purcell, S T

    2014-03-28

    We present here well-defined Coulomb staircases using an original field-emission experiment on several individual in situ-grown single-wall carbon nanotubes. A unique in situ process was applied nine times to progressively shorten one single-wall carbon nanotube down to ≃10  nm, which increased the oscillations periods from 5.5 to 80 V, the temperature for observable Coulomb staircase to 1100 K and the currents to 1.8  μA. This process led to the brightest electron source ever reported [9×1011  A/(str m2 V)].

  6. Distinct Cellular Assembly Stoichiometry of Polycomb Complexes on Chromatin Revealed by Single-molecule Chromatin Immunoprecipitation Imaging*♦

    Science.gov (United States)

    Tatavosian, Roubina; Zhen, Chao Yu; Duc, Huy Nguyen; Balas, Maggie M.; Johnson, Aaron M.; Ren, Xiaojun

    2015-01-01

    Epigenetic complexes play an essential role in regulating chromatin structure, but information about their assembly stoichiometry on chromatin within cells is poorly understood. The cellular assembly stoichiometry is critical for appreciating the initiation, propagation, and maintenance of epigenetic inheritance during normal development and in cancer. By combining genetic engineering, chromatin biochemistry, and single-molecule fluorescence imaging, we developed a novel and sensitive approach termed single-molecule chromatin immunoprecipitation imaging (Sm-ChIPi) to enable investigation of the cellular assembly stoichiometry of epigenetic complexes on chromatin. Sm-ChIPi was validated by using chromatin complexes with known stoichiometry. The stoichiometry of subunits within a polycomb complex and the assembly stoichiometry of polycomb complexes on chromatin have been extensively studied but reached divergent views. Moreover, the cellular assembly stoichiometry of polycomb complexes on chromatin remains unexplored. Using Sm-ChIPi, we demonstrated that within mouse embryonic stem cells, one polycomb repressive complex (PRC) 1 associates with multiple nucleosomes, whereas two PRC2s can bind to a single nucleosome. Furthermore, we obtained direct physical evidence that the nucleoplasmic PRC1 is monomeric, whereas PRC2 can dimerize in the nucleoplasm. We showed that ES cell differentiation induces selective alteration of the assembly stoichiometry of Cbx2 on chromatin but not other PRC1 components. We additionally showed that the PRC2-mediated trimethylation of H3K27 is not required for the assembly stoichiometry of PRC1 on chromatin. Thus, these findings uncover that PRC1 and PRC2 employ distinct mechanisms to assemble on chromatin, and the novel Sm-ChIPi technique could provide single-molecule insight into other epigenetic complexes. PMID:26381410

  7. Transcriptional networks in single perivascular cells sorted from human adipose tissue reveal a hierarchy of mesenchymal stem cells.

    Science.gov (United States)

    Hardy, W Reef; Moldovan, Nicanor I; Moldovan, Leni; Livak, Kenneth J; Datta; Goswami, Chirayu; Corselli, Mirko; Traktuev, Dmitry O; Murray, Iain R; Péault, Bruno; March, Keith

    2017-02-24

    Adipose tissue is a rich source of multipotent mesenchymal stem-like cells, located in the perivascular niche. Based on their surface markers, these have been assigned to two main categories: CD34+CD31-CD45-CD146- cells (adventitial stromal/stem cells, ASCs), and CD146+CD31-CD34-CD45- cells (pericytes, PCs). These populations display heterogeneity of unknown significance. We hypothesized that aldehyde dehydrogenase (ALDH) activity, a functional marker of primitivity, could help to better define ASC and PC subclasses. To this end, the stromal vascular fraction from a human lipoaspirate was simultaneously stained with fluorescent antibodies to CD31, CD45, CD34, and CD146 antigens and the ALDH substrate Aldefluor®, then sorted by FACS. Individual ASCs (n=67) and PCs (n=73) selected from the extremities of the ALDH-staining spectrum were transcriptionally profiled by Fluidigm single-cell quantitative PCR for a predefined set (n=429) of marker genes. To these single-cell data, we applied differential expression and principal component and clustering analysis, as well as an original gene co-expression network reconstruction algorithm. Despite the stochasticity at the single-cell level, covariation gene expression analysis yielded multiple network connectivity parameters suggesting that these perivascular progenitor cell subclasses possess the following order of maturity: i) ALDH(br) ASC (most primitive); ii) ALDH(dim) ASC; iii) ALDH(br) PC; iv) ALDH(dim) PC (least primitive). This order was independently supported by specific combinations of class-specific expressed genes and further confirmed by the analysis of associated signaling pathways. In conclusion, single-cell transcriptional analysis of four populations isolated from fat by surface markers and enzyme activity suggests a developmental hierarchy among perivascular mesenchymal stem cells supported by markers and co-expression networks. This article is protected by copyright. All rights reserved.

  8. A novel single virus infection system reveals that influenza virus preferentially infects cells in g1 phase.

    Directory of Open Access Journals (Sweden)

    Ryuta Ueda

    Full Text Available BACKGROUND: Influenza virus attaches to sialic acid residues on the surface of host cells via the hemagglutinin (HA, a glycoprotein expressed on the viral envelope, and enters into the cytoplasm by receptor-mediated endocytosis. The viral genome is released and transported in to the nucleus, where transcription and replication take place. However, cellular factors affecting the influenza virus infection such as the cell cycle remain uncharacterized. METHODS/RESULTS: To resolve the influence of cell cycle on influenza virus infection, we performed a single-virus infection analysis using optical tweezers. Using this newly developed single-virus infection system, the fluorescence-labeled influenza virus was trapped on a microchip using a laser (1064 nm at 0.6 W, transported, and released onto individual H292 human lung epithelial cells. Interestingly, the influenza virus attached selectively to cells in the G1-phase. To clarify the molecular differences between cells in G1- and S/G2/M-phase, we performed several physical and chemical assays. Results indicated that: 1 the membranes of cells in G1-phase contained greater amounts of sialic acids (glycoproteins than the membranes of cells in S/G2/M-phase; 2 the membrane stiffness of cells in S/G2/M-phase is more rigid than those in G1-phase by measurement using optical tweezers; and 3 S/G2/M-phase cells contained higher content of Gb3, Gb4 and GlcCer than G1-phase cells by an assay for lipid composition. CONCLUSIONS: A novel single-virus infection system was developed to characterize the difference in influenza virus susceptibility between G1- and S/G2/M-phase cells. Differences in virus binding specificity were associated with alterations in the lipid composition, sialic acid content, and membrane stiffness. This single-virus infection system will be useful for studying the infection mechanisms of other viruses.

  9. Distinct Cellular Assembly Stoichiometry of Polycomb Complexes on Chromatin Revealed by Single-molecule Chromatin Immunoprecipitation Imaging.

    Science.gov (United States)

    Tatavosian, Roubina; Zhen, Chao Yu; Duc, Huy Nguyen; Balas, Maggie M; Johnson, Aaron M; Ren, Xiaojun

    2015-11-20

    Epigenetic complexes play an essential role in regulating chromatin structure, but information about their assembly stoichiometry on chromatin within cells is poorly understood. The cellular assembly stoichiometry is critical for appreciating the initiation, propagation, and maintenance of epigenetic inheritance during normal development and in cancer. By combining genetic engineering, chromatin biochemistry, and single-molecule fluorescence imaging, we developed a novel and sensitive approach termed single-molecule chromatin immunoprecipitation imaging (Sm-ChIPi) to enable investigation of the cellular assembly stoichiometry of epigenetic complexes on chromatin. Sm-ChIPi was validated by using chromatin complexes with known stoichiometry. The stoichiometry of subunits within a polycomb complex and the assembly stoichiometry of polycomb complexes on chromatin have been extensively studied but reached divergent views. Moreover, the cellular assembly stoichiometry of polycomb complexes on chromatin remains unexplored. Using Sm-ChIPi, we demonstrated that within mouse embryonic stem cells, one polycomb repressive complex (PRC) 1 associates with multiple nucleosomes, whereas two PRC2s can bind to a single nucleosome. Furthermore, we obtained direct physical evidence that the nucleoplasmic PRC1 is monomeric, whereas PRC2 can dimerize in the nucleoplasm. We showed that ES cell differentiation induces selective alteration of the assembly stoichiometry of Cbx2 on chromatin but not other PRC1 components. We additionally showed that the PRC2-mediated trimethylation of H3K27 is not required for the assembly stoichiometry of PRC1 on chromatin. Thus, these findings uncover that PRC1 and PRC2 employ distinct mechanisms to assemble on chromatin, and the novel Sm-ChIPi technique could provide single-molecule insight into other epigenetic complexes.

  10. Single-cell Transcriptional Analysis Reveals Novel Neuronal Phenotypes and Interaction Networks involved In the Central Circadian Clock

    Directory of Open Access Journals (Sweden)

    James Park

    2016-10-01

    Full Text Available Single-cell heterogeneity confounds efforts to understand how a population of cells organizes into cellular networks that underlie tissue-level function. This complexity is prominent in the mammalian suprachiasmatic nucleus (SCN. Here, individual neurons exhibit a remarkable amount of asynchronous behavior and transcriptional heterogeneity. However, SCN neurons are able to generate precisely coordinated synaptic and molecular outputs that synchronize the body to a common circadian cycle by organizing into cellular networks. To understand this emergent cellular network property, it is important to reconcile single-neuron heterogeneity with network organization. In light of recent studies suggesting that transcriptionally heterogeneous cells organize into distinct cellular phenotypes, we characterized the transcriptional, spatial, and functional organization of 352 SCN neurons from mice experiencing phase-shifts in their circadian cycle. Using the community structure detection method and multivariate analytical techniques, we identified previously undescribed neuronal phenotypes that are likely to participate in regulatory networks with known SCN cell types. Based on the newly discovered neuronal phenotypes, we developed a data-driven neuronal network structure in which multiple cell types interact through known synaptic and paracrine signaling mechanisms. These results provide a basis from which to interpret the functional variability of SCN neurons and describe methodologies towards understanding how a population of heterogeneous single cells organizes into cellular networks that underlie tissue-level function.

  11. Near-unity coupling efficiency of a quantum emitter to a photonic crystal waveguide.

    Science.gov (United States)

    Arcari, M; Söllner, I; Javadi, A; Lindskov Hansen, S; Mahmoodian, S; Liu, J; Thyrrestrup, H; Lee, E H; Song, J D; Stobbe, S; Lodahl, P

    2014-08-29

    A quantum emitter efficiently coupled to a nanophotonic waveguide constitutes a promising system for the realization of single-photon transistors, quantum-logic gates based on giant single-photon nonlinearities, and high bit-rate deterministic single-photon sources. The key figure of merit for such devices is the β factor, which is the probability for an emitted single photon to be channeled into a desired waveguide mode. We report on the experimental achievement of β=98.43%±0.04% for a quantum dot coupled to a photonic crystal waveguide, corresponding to a single-emitter cooperativity of η=62.7±1.5. This constitutes a nearly ideal photon-matter interface where the quantum dot acts effectively as a 1D "artificial" atom, since it interacts almost exclusively with just a single propagating optical mode. The β factor is found to be remarkably robust to variations in position and emission wavelength of the quantum dots. Our work demonstrates the extraordinary potential of photonic crystal waveguides for highly efficient single-photon generation and on-chip photon-photon interaction.

  12. Theory and measurements of emittance preservation in plasma wakefield acceleration

    Energy Technology Data Exchange (ETDEWEB)

    Frederico, Joel

    2016-12-01

    In this dissertation, we examine the preservation and measurement of emittance in the plasma wakefield acceleration blowout regime. Plasma wakefield acceleration (PWFA) is a revolutionary approach to accelerating charged particles that has been demonstrated to have the potential for gradients orders of magnitude greater than traditional approaches. The application of PWFA to the design of a linear collider will make new high energy physics research possible, but the design parameters must first be shown to be competitive with traditional methods. Emittance preservation is necessary in the design of a linear collider in order to maximize luminosity. We examine the conditions necessary for circular symmetry in the PWFA blowout regime, and demonstrate that current proposals meet these bounds. We also present an application of beam lamentation which describes the process of beam parameter and emittance matching. We show that the emittance growth saturates as a consequence of energy spread in the beam. The initial beam parameters determine the amount of emittance growth, while the contribution of energy spread is negligible. We also present a model for ion motion in the presence of a beam that is much more dense than the plasma. By combining the model of ion motion and emittance growth, we find the emittance growth due to ion motion is minimal in the case of marginal ion motion. In addition, we present a simulation that validates the ion motion model, which is under further development to examine emittance growth of both marginal and pronounced ion motion. Finally, we present a proof-of-concept of an emittance measurement which may enable the analysis of emittance preservation in future PWFA experiments.

  13. Mesoscopic quantum emitters coupled to plasmonic nanostructures

    DEFF Research Database (Denmark)

    Andersen, Mads Lykke

    This thesis reports research on quantum dots coupled to dielectric and plasmonic nano-structures by way of nano-structure fabrication, optical measurements, and theoretical modeling. To study light-matter interaction, plasmonic gap waveguides with nanometer dimensions as well as samples for studies...... of quantum dots in proximity to semiconductor/air and semiconductor/metal interfaces, were fabricated. We measured the decay dynamics of quantum dots near plasmonic gap waveguides and observed modied decay rates. The obtainable modications with the fabricated structures are calculated to be too small...... for the spontaneous emission of mesoscopic quantum emitters is developed. The light-matter interaction is in this model modied beyond the dipole expectancy and found to both suppress and enhance the coupling to plasmonic modes in excellent agreement with our measurements. We demonstrate that this mesoscopic effect...

  14. A Reliable and Simple Method for Fabricating a Poly(Dimethylsiloxane) Electrospray Ionization Chip with a Corner-Integrated Emitter

    Science.gov (United States)

    Qian, Xiang; Xu, Jie; Yu, Cilong; Chen, Yan; Yu, Quan; Ni, Kai; Wang, Xiaohao

    2015-01-01

    Monolithically integrated emitters have been increasingly applied to microfluidic devices that are coupled to mass spectrometers (MS) as electrospray ionization sources (ESI). A new method was developed to fabricate a duplicable structure which integrated the emitter into a poly(dimethylsiloxane) chip corner. Two photoresist layers containing a raised base which guaranteed the precise integration of the electrospray tip emitter and ensured that the cutting out of the tip exerted no influence even during repeated prototyping were used to ease the operation of the process. Highly stable ESI-MS performance was obtained and the results were compared with those of a commercial fused-silica capillary source. Furthermore, chip-to-chip and run-to-run results indicated both reliability and reproducibility during repeated fabrication. These results reveal that the proposed chip can provide an ideal ion source for MS across many applications, especially with the perspective to be widely used in portable MS during on-site analysis. PMID:25894936

  15. A compact time reversal emitter-receiver based on a leaky random cavity

    Science.gov (United States)

    Luong, Trung-Dung; Hies, Thomas; Ohl, Claus-Dieter

    2016-11-01

    Time reversal acoustics (TRA) has gained widespread applications for communication and measurements. In general, a scattering medium in combination with multiple transducers is needed to achieve a sufficiently large acoustical aperture. In this paper, we report an implementation for a cost-effective and compact time reversal emitter-receiver driven by a single piezoelectric element. It is based on a leaky cavity with random 3-dimensional printed surfaces. The random surfaces greatly increase the spatio-temporal focusing quality as compared to flat surfaces and allow the focus of an acoustic beam to be steered over an angle of 41°. We also demonstrate its potential use as a scanner by embedding a receiver to detect an object from its backscatter without moving the TRA emitter.

  16. Fast electrical switching of orbital angular momentum modes using ultra-compact integrated vortex emitters.

    Science.gov (United States)

    Strain, Michael J; Cai, Xinlun; Wang, Jianwei; Zhu, Jiangbo; Phillips, David B; Chen, Lifeng; Lopez-Garcia, Martin; O'Brien, Jeremy L; Thompson, Mark G; Sorel, Marc; Yu, Siyuan

    2014-09-17

    The ability to rapidly switch between orbital angular momentum modes of light has important implications for future classical and quantum systems. In general, orbital angular momentum beams are generated using free-space bulk optical components where the fastest reconfiguration of such systems is around a millisecond using spatial light modulators. In this work, an extremely compact optical vortex emitter is demonstrated with the ability to actively tune between different orbital angular momentum modes. The emitter is tuned using a single electrically contacted thermo-optical control, maintaining device simplicity and micron scale footprint. On-off keying and orbital angular momentum mode switching are achieved at rates of 10 μs and 20 μs respectively.

  17. Suppression of Emittance Growth Using a Shaped Cold Atom Electron and Ion Source

    Science.gov (United States)

    Thompson, D. J.; Murphy, D.; Speirs, R. W.; van Bijnen, R. M. W.; McCulloch, A. J.; Scholten, R. E.; Sparkes, B. M.

    2016-11-01

    We demonstrate precise control of charged particle bunch shape with a cold atom electron and ion source to create bunches with linear and, therefore, reversible Coulomb expansion. Using ultracold charged particles enables detailed observation of space-charge effects without loss of information from thermal diffusion, unambiguously demonstrating that shaping in three dimensions can result in a marked reduction of Coulomb-driven emittance growth. We show that the emittance growth suppression is accompanied by an increase in bunch focusability and brightness, improvements necessary for the development of sources capable of coherent single-shot ultrafast electron diffraction of noncrystalline objects, with applications ranging from femtosecond chemistry to materials science and rational drug design.

  18. Structure predictions of two Bauhinia variegata lectins reveal patterns of C-terminal properties in single chain legume lectins.

    Science.gov (United States)

    Moreira, Gustavo M S G; Conceição, Fabricio R; McBride, Alan J A; Pinto, Luciano da S

    2013-01-01

    Bauhinia variegata lectins (BVL-I and BVL-II) are single chain lectins isolated from the plant Bauhinia variegata. Single chain lectins undergo post-translational processing on its N-terminal and C-terminal regions, which determines their physiological targeting, carbohydrate binding activity and pattern of quaternary association. These two lectins are isoforms, BVL-I being highly glycosylated, and thus far, it has not been possible to determine their structures. The present study used prediction and validation algorithms to elucidate the likely structures of BVL-I and -II. The program Bhageerath-H was chosen from among three different structure prediction programs due to its better overall reliability. In order to predict the C-terminal region cleavage sites, other lectins known to have this modification were analysed and three rules were created: (1) the first amino acid of the excised peptide is small or hydrophobic; (2) the cleavage occurs after an acid, polar, or hydrophobic residue, but not after a basic one; and (3) the cleavage spot is located 5-8 residues after a conserved Leu amino acid. These rules predicted that BVL-I and -II would have fifteen C-terminal residues cleaved, and this was confirmed experimentally by Edman degradation sequencing of BVL-I. Furthermore, the C-terminal analyses predicted that only BVL-II underwent α-helical folding in this region, similar to that seen in SBA and DBL. Conversely, BVL-I and -II contained four conserved regions of a GS-I association, providing evidence of a previously undescribed X4+unusual oligomerisation between the truncated BVL-I and the intact BVL-II. This is the first report on the structural analysis of lectins from Bauhinia spp. and therefore is important for the characterisation C-terminal cleavage and patterns of quaternary association of single chain lectins.

  19. Structure predictions of two Bauhinia variegata lectins reveal patterns of C-terminal properties in single chain legume lectins.

    Directory of Open Access Journals (Sweden)

    Gustavo M S G Moreira

    Full Text Available Bauhinia variegata lectins (BVL-I and BVL-II are single chain lectins isolated from the plant Bauhinia variegata. Single chain lectins undergo post-translational processing on its N-terminal and C-terminal regions, which determines their physiological targeting, carbohydrate binding activity and pattern of quaternary association. These two lectins are isoforms, BVL-I being highly glycosylated, and thus far, it has not been possible to determine their structures. The present study used prediction and validation algorithms to elucidate the likely structures of BVL-I and -II. The program Bhageerath-H was chosen from among three different structure prediction programs due to its better overall reliability. In order to predict the C-terminal region cleavage sites, other lectins known to have this modification were analysed and three rules were created: (1 the first amino acid of the excised peptide is small or hydrophobic; (2 the cleavage occurs after an acid, polar, or hydrophobic residue, but not after a basic one; and (3 the cleavage spot is located 5-8 residues after a conserved Leu amino acid. These rules predicted that BVL-I and -II would have fifteen C-terminal residues cleaved, and this was confirmed experimentally by Edman degradation sequencing of BVL-I. Furthermore, the C-terminal analyses predicted that only BVL-II underwent α-helical folding in this region, similar to that seen in SBA and DBL. Conversely, BVL-I and -II contained four conserved regions of a GS-I association, providing evidence of a previously undescribed X4+unusual oligomerisation between the truncated BVL-I and the intact BVL-II. This is the first report on the structural analysis of lectins from Bauhinia spp. and therefore is important for the characterisation C-terminal cleavage and patterns of quaternary association of single chain lectins.

  20. Single-molecule visualization of Saccharomyces cerevisiae leading-strand synthesis reveals dynamic interaction between MTC and the replisome.

    Science.gov (United States)

    Lewis, Jacob S; Spenkelink, Lisanne M; Schauer, Grant D; Hill, Flynn R; Georgescu, Roxanna E; O'Donnell, Michael E; van Oijen, Antoine M

    2017-09-18

    The replisome, the multiprotein system responsible for genome duplication, is a highly dynamic complex displaying a large number of different enzyme activities. Recently, the Saccharomyces cerevisiae minimal replication reaction has been successfully reconstituted in vitro. This provided an opportunity to uncover the enzymatic activities of many of the components in a eukaryotic system. Their dynamic behavior and interactions in the context of the replisome, however, remain unclear. We use a tethered-bead assay to provide real-time visualization of leading-strand synthesis by the S. cerevisiae replisome at the single-molecule level. The minimal reconstituted leading-strand replisome requires 24 proteins, forming the CMG helicase, the Pol ε DNA polymerase, the RFC clamp loader, the PCNA sliding clamp, and the RPA single-stranded DNA binding protein. We observe rates and product lengths similar to those obtained from ensemble biochemical experiments. At the single-molecule level, we probe the behavior of two components of the replication progression complex and characterize their interaction with active leading-strand replisomes. The Minichromosome maintenance protein 10 (Mcm10), an important player in CMG activation, increases the number of productive replication events in our assay. Furthermore, we show that the fork protection complex Mrc1-Tof1-Csm3 (MTC) enhances the rate of the leading-strand replisome threefold. The introduction of periods of fast replication by MTC leads to an average rate enhancement of a factor of 2, similar to observations in cellular studies. We observe that the MTC complex acts in a dynamic fashion with the moving replisome, leading to alternating phases of slow and fast replication.

  1. Single-cell genomics reveals the lifestyle of Poribacteria, a candidate phylum symbiotically associated with marine sponges

    Science.gov (United States)

    Siegl, Alexander; Kamke, Janine; Hochmuth, Thomas; Piel, Jörn; Richter, Michael; Liang, Chunguang; Dandekar, Thomas; Hentschel, Ute

    2011-01-01

    In this study, we present a single-cell genomics approach for the functional characterization of the candidate phylum Poribacteria, members of which are nearly exclusively found in marine sponges. The microbial consortia of the Mediterranean sponge Aplysina aerophoba were singularized by fluorescence-activated cell sorting, and individual microbial cells were subjected to phi29 polymerase-mediated ‘whole-genome amplification'. Pyrosequencing of a single amplified genome (SAG) derived from a member of the Poribacteria resulted in nearly 1.6 Mb of genomic information distributed among 554 contigs analyzed in this study. Approximately two-third of the poribacterial genome was sequenced. Our findings shed light on the functional properties and lifestyle of a possibly ancient bacterial symbiont of marine sponges. The Poribacteria are mixotrophic bacteria with autotrophic CO2-fixation capacities through the Wood–Ljungdahl pathway. The cell wall is of Gram-negative origin. The Poribacteria produce at least two polyketide synthases (PKSs), one of which is the sponge-specific Sup-type PKS. Several putative symbiosis factors such as adhesins (bacterial Ig-like domains, lamininin G domain proteins), adhesin-related proteins (ankyrin, fibronectin type III) and tetratrico peptide repeat domain-encoding proteins were identified, which might be involved in mediating sponge–microbe interactions. The discovery of genes coding for 24-isopropyl steroids implies that certain fossil biomarkers used to date the origins of metazoan life on earth may possibly be of poribacterial origin. Single-cell genomic approaches, such as those shown herein, contribute to a better understanding of beneficial microbial consortia, of which most members are, because of the lack of cultivation, inaccessible by conventional techniques. PMID:20613790

  2. Single-cell genomics reveals the lifestyle of Poribacteria, a candidate phylum symbiotically associated with marine sponges.

    Science.gov (United States)

    Siegl, Alexander; Kamke, Janine; Hochmuth, Thomas; Piel, Jörn; Richter, Michael; Liang, Chunguang; Dandekar, Thomas; Hentschel, Ute

    2011-01-01

    In this study, we present a single-cell genomics approach for the functional characterization of the candidate phylum Poribacteria, members of which are nearly exclusively found in marine sponges. The microbial consortia of the Mediterranean sponge Aplysina aerophoba were singularized by fluorescence-activated cell sorting, and individual microbial cells were subjected to phi29 polymerase-mediated 'whole-genome amplification'. Pyrosequencing of a single amplified genome (SAG) derived from a member of the Poribacteria resulted in nearly 1.6 Mb of genomic information distributed among 554 contigs analyzed in this study. Approximately two-third of the poribacterial genome was sequenced. Our findings shed light on the functional properties and lifestyle of a possibly ancient bacterial symbiont of marine sponges. The Poribacteria are mixotrophic bacteria with autotrophic CO(2)-fixation capacities through the Wood-Ljungdahl pathway. The cell wall is of Gram-negative origin. The Poribacteria produce at least two polyketide synthases (PKSs), one of which is the sponge-specific Sup-type PKS. Several putative symbiosis factors such as adhesins (bacterial Ig-like domains, lamininin G domain proteins), adhesin-related proteins (ankyrin, fibronectin type III) and tetratrico peptide repeat domain-encoding proteins were identified, which might be involved in mediating sponge-microbe interactions. The discovery of genes coding for 24-isopropyl steroids implies that certain fossil biomarkers used to date the origins of metazoan life on earth may possibly be of poribacterial origin. Single-cell genomic approaches, such as those shown herein, contribute to a better understanding of beneficial microbial consortia, of which most members are, because of the lack of cultivation, inaccessible by conventional techniques.

  3. Dynamic micro-organization of P2X7 receptors revealed by PALM based single particle tracking

    OpenAIRE

    Shrivastava, Amulya N.; Rodriguez, Pamela C.; Triller, Antoine; Renner, Marianne

    2013-01-01

    Adenosine triphosphate (ATP)-gated P2X7 receptors (P2X7Rs) are members of the purinergic receptor family that are expressed in several cell types including neurons. A high concentration of ATP is required for the channel opening of P2X7Rs compared to other members of this receptor family. Recent work suggests that ATP binding to members of the P2X receptor family determines the diffusion and localization of these receptors on the plasma membrane of neurons. Here, we employed single particle t...

  4. Physical electrostatics of small field emitter arrays/clusters

    Science.gov (United States)

    Forbes, Richard G.

    2016-08-01

    This paper aims to improve qualitative understanding of electrostatic influences on apex field enhancement factors (AFEFs) for small field emitter arrays/clusters. Using the "floating sphere at emitter-plate potential" (FSEPP) model, it re-examines the electrostatics and mathematics of three simple systems of identical post-like emitters. For the isolated emitter, various approaches are noted. An adequate approximation is to consider only the effects of sphere charges and (for significantly separated emitters) image charges. For the 2-emitter system, formulas are found for charge-transfer ("charge-blunting") effects and neighbor-field effects, for widely spaced and for "sufficiently closely spaced" emitters. Mutual charge-blunting is always the dominant effect, with a related (negative) fractional AFEF-change δtwo. For sufficiently small emitter spacing c, |δtwo| varies approximately as 1/c; for large spacing, |δtwo| decreases as 1/c3. In a 3-emitter equispaced linear array, differential charge-blunting and differential neighbor-field effects occur, but differential charge-blunting effects are dominant, and cause the "exposed" outer emitters to have higher AFEF (γ0) than the central emitter (γ1). Formulas are found for the exposure ratio Ξ = γ0/γ1, for large and for sufficiently small separations. The FSEPP model for an isolated emitter has accuracy around 30%. Line-charge models (LCMs) are an alternative, but an apparent difficulty with recent LCM implementations is identified. Better descriptions of array electrostatics may involve developing good fitting equations for AFEFs derived from accurate numerical solution of Laplace's equation, perhaps with equation form(s) guided qualitatively by FSEPP-model results. In existing fitting formulas, the AFEF-reduction decreases exponentially as c increases, which is different from the FSEPP-model formulas. This discrepancy needs to be investigated, using systematic Laplace-based simulations and appropriate results

  5. Experimental Demonstration of a Hybrid-Quantum-Emitter Producing Individual Entangled Photon Pairs in the Telecom Band

    Science.gov (United States)

    Chen, Geng; Zou, Yang; Zhang, Wen-Hao; Zhang, Zi-Huai; Zhou, Zong-Quan; He, De-Yong; Tang, Jian-Shun; Liu, Bi-Heng; Yu, Ying; Zha, Guo-Wei; Ni, Hai-Qiao; Niu, Zhi-Chuan; Han, Yong-Jian; Li, Chuan-Feng; Guo, Guang-Can

    2016-05-01

    Quantum emitters generating individual entangled photon pairs (IEPP) have significant fundamental advantages over schemes that suffer from multiple photon emission, or schemes that require post-selection techniques or the use of photon-number discriminating detectors. Quantum dots embedded within nanowires (QD-NWs) represent one of the most promising candidate for quantum emitters that provide a high collection efficiency of photons. However, a quantum emitter that generates IEPP in the telecom band is still an issue demanding a prompt solution. Here, we demonstrate in principle that IEPPs in the telecom band can be created by combining a single QD-NW and a nonlinear crystal waveguide. The QD-NW system serves as the single photon source, and the emitted visible single photons are split into IEPPs at approximately 1.55 μm through the process of spontaneous parametric down conversion (SPDC) in a periodically poled lithium niobate (PPLN) waveguide. The compatibility of the QD-PPLN interface is the determinant factor in constructing this novel hybrid-quantum-emitter (HQE). Benefiting from the desirable optical properties of QD-NWs and the extremely high nonlinear conversion efficiency of PPLN waveguides, we successfully generate IEPPs in the telecom band with the polarization degree of freedom. The entanglement of the generated photon pairs is confirmed by the entanglement witness. Our experiment paves the way to producing HQEs inheriting the advantages of multiple systems.

  6. Tuning the spectral emittance of α-SiC open-cell foams up to 1300 K with their macro porosity

    Directory of Open Access Journals (Sweden)

    B. Rousseau

    2016-06-01

    Full Text Available A simple and robust analytical model is used to finely predict the spectral emittance under air up to 1300 K of α-SiC open-cell foams constituted of optically thick struts. The model integrates both the chemical composition and the macro-porosity and is valid only if foams have volumes higher than their Representative Elementary Volumes required for determining their emittance. Infrared emission spectroscopy carried out on a doped silicon carbide single crystal associated to homemade numerical tools based on 3D meshed images (Monte Carlo Ray Tracing code, foam generator make possible to understand the exact role of the cell network in emittance. Finally, one can tune the spectral emittance of α-SiC foams up to 1300 K by simply changing their porosity.

  7. Tuning the spectral emittance of α-SiC open-cell foams up to 1300 K with their macro porosity

    Science.gov (United States)

    Rousseau, B.; Guevelou, S.; Mekeze-Monthe, A.; Vicente, J.; Del Campo, L.; De Sousa Meneses, D.; Echegut, P.; Caliot, C.; Flamant, G.

    2016-06-01

    A simple and robust analytical model is used to finely predict the spectral emittance under air up to 1300 K of α-SiC open-cell foams constituted of optically thick struts. The model integrates both the chemical composition and the macro-porosity and is valid only if foams have volumes higher than their Representative Elementary Volumes required for determining their emittance. Infrared emission spectroscopy carried out on a doped silicon carbide single crystal associated to homemade numerical tools based on 3D meshed images (Monte Carlo Ray Tracing code, foam generator) make possible to understand the exact role of the cell network in emittance. Finally, one can tune the spectral emittance of α-SiC foams up to 1300 K by simply changing their porosity.

  8. Harmonic force spectroscopy reveals a force-velocity curve from a single human beta cardiac myosin motor

    Science.gov (United States)

    Sung, Jongmin; Nag, Suman; Vestergaard, Christian; Mortensen, Kim; Flyvbjerg, Henrik; Spudich, James

    2014-03-01

    A muscle contracts rapidly under low load, but slowly under high load. Its molecular mechanisms remain to be elucidated, however. During contraction, myosins in thick filaments interact with actin in thin filaments in the sarcomere, cycling between a strongly bound (force producing) state and a weakly bound (relaxed) state. Huxley et al. have previously proposed that the transition from the strong to the weak interaction can be modulated by a load. We use a new method we call ``harmonic force spectroscopy'' to extract a load-velocity curve from a single human beta cardiac myosin II motor. With a dual-beam optical trap, we hold an actin dumbbell over a myosin molecule anchored to the microscope stage that oscillates sinusoidally. Upon binding, the motor experiences an oscillatory load with a mean that is directed forward or backward, depending on binding location We find that the bound time at saturating [ATP] is exponentially correlated with the mean load, which is explained by Arrhenius transition theory. With a stroke size measurement, we obtained a load-velocity curve from a single myosin. We compare the curves for wild-type motors with mutants that cause hypertrophic cardiomyopathies, to understand the effects on the contractile cycle

  9. Binding and movement of individual Cel7A cellobiohydrolases on crystalline cellulose surfaces revealed by single-molecule fluorescence imaging.

    Science.gov (United States)

    Jung, Jaemyeong; Sethi, Anurag; Gaiotto, Tiziano; Han, Jason J; Jeoh, Tina; Gnanakaran, Sandrasegaram; Goodwin, Peter M

    2013-08-16

    The efficient catalytic conversion of biomass to bioenergy would meet a large portion of energy requirements in the near future. A crucial step in this process is the enzyme-catalyzed hydrolysis of cellulose to glucose that is then converted into fuel such as ethanol by fermentation. Here we use single-molecule fluorescence imaging to directly monitor the movement of individual Cel7A cellobiohydrolases from Trichoderma reesei (TrCel7A) on the surface of insoluble cellulose fibrils to elucidate molecular level details of cellulase activity. The motion of multiple, individual TrCel7A cellobiohydrolases was simultaneously recorded with ∼15-nm spatial resolution. Time-resolved localization microscopy provides insights on the activity of TrCel7A on cellulose and informs on nonproductive binding and diffusion. We measured single-molecule residency time distributions of TrCel7A bound to cellulose both in the presence of and absence of cellobiose the major product and a potent inhibitor of Cel7A activity. Combining these results with a kinetic model of TrCel7A binding provides microscopic insight into interactions between TrCel7A and the cellulose substrate.

  10. Dopant profile control of epitaxial emitter for silicon solar cells by low temperature epitaxy

    Science.gov (United States)

    Lai, Donny; Tan, Yew Heng; Gunawan, Oki; He, Lining; Seng Tan, Chuan

    2011-07-01

    We report an alternative approach to grow phosphorus-doped epitaxial silicon emitter by rapid thermal chemical vapor deposition at low temperature (T ≥ 700 °C). A power conversion efficiency (PCE) of (6.6 ± 0.3)% and a pseudo PCE of (10.2 ± 0.2)% has been achieved for the solar cell with epi-emitter grown at 700 °C, in the absence of surface texturization, antireflective coating, and back surface field enhancement, without considering front contact shading. Secondary ion mass spectroscopy revealed that lower temperature silicon epitaxy yields a more abrupt p-n junction, suggesting potential applications for radial p-n junction wire array solar cells.

  11. A Variable Single Photon Plasmonic Beamsplitter

    DEFF Research Database (Denmark)

    Israelsen, Niels Møller; Kumar, Shailesh; Huck, Alexander

    Plasmonic structures can both be exploited for scaling down optical components beyond the diffraction limit and enhancing andcollecting the emission from a single dipole emitter. Here, we experimentally demonstrate adiabatic coupling between two silvernanowires using a nitrogen vacancy center...

  12. Low-emittance tuning at the Cornell Electron Storage Ring

    CERN Document Server

    Shanks, James; Sagan, David

    2013-01-01

    In 2008 the Cornell Electron/Positron Storage Ring (CESR) was reconfigured from an electron/positron collider to serve as a testbed for the International Linear Collider (ILC) damping rings. One of the primary goals of the CESR Test Accelerator (CesrTA) project is to develop low emittance tuning techniques to achieve sub-10pm geometric vertical emittance at 2.085 GeV. This paper discusses the tuning methods used at CesrTA to achieve low-emittance conditions. A minimum vertical emittance of 8.7 +2.9/-3.4(sys) +/-0.2(stat) pm has been achieved at 2.085 GeV. In various configurations and beam energies the correction technique routinely achieves vertical emittance <15 pm after correction. Beam-based measurement and correction requires about 15 minutes. Simulations modeling the effects of magnet misalignments, BPM errors, and emittance correction algorithm suggest the residual vertical emittance measured at the conclusion of the tuning procedure is dominated by sources other than optics errors and misalignments...

  13. Microsatellite Primers for Parkia biglobosa (Fabaceae: Mimosoideae Reveal that a Single Plant Sires All Seeds Per Pod

    Directory of Open Access Journals (Sweden)

    Kristin Marie Lassen

    2014-06-01

    Full Text Available Premise of the study: Microsatellite primers were developed for an indigenous fruit tree, Parkia biglobosa, as a tool to study reproductive biology and population structure. Here we use the primers to determine the number of fathers per pod. Methods and Results: Microsatellite loci were enriched in a genomic sample and isolated using pyrosequencing. Eleven primer pairs were characterized in two populations of P. biglobosa in Burkina Faso (each with 40 trees. The number of alleles per locus ranged from eight to 15, and one locus had null alleles. We genotyped seeds from 24 open-pollinated pods. The genotypic profiles of seeds per pod suggest that all seeds are outcrossed and that only one pollen donor sires all ovules in a single fruit. Conclusions: Ten microsatellite markers were highly polymorphic. All seeds per pod of P. biglobosa were full siblings. The markers will be useful for reproductive and population genetic studies.

  14. Microsatellite primers for Parkia biglobosa (Fabaceae: Mimosoideae) reveal that a single plant sires all seeds per pod1

    Science.gov (United States)

    Lassen, Kristin Marie; Kjær, Erik Dahl; Ouédraogo, Moussa; Nielsen, Lene Rostgaard

    2014-01-01

    • Premise of the study: Microsatellite primers were developed for an indigenous fruit tree, Parkia biglobosa, as a tool to study reproductive biology and population structure. Here we use the primers to determine the number of fathers per pod. • Methods and Results: Microsatellite loci were enriched in a genomic sample and isolated using pyrosequencing. Eleven primer pairs were characterized in two populations of P. biglobosa in Burkina Faso (each with 40 trees). The number of alleles per locus ranged from eight to 15, and one locus had null alleles. We genotyped seeds from 24 open-pollinated pods. The genotypic profiles of seeds per pod suggest that all seeds are outcrossed and that only one pollen donor sires all ovules in a single fruit. • Conclusions: Ten microsatellite markers were highly polymorphic. All seeds per pod of P. biglobosa were full siblings. The markers will be useful for reproductive and population genetic studies. PMID:25202634

  15. Duplication of a Single Neuron in C. elegans Reveals a Pathway for Dendrite Tiling by Mutual Repulsion

    Directory of Open Access Journals (Sweden)

    Zhiqi Candice Yip

    2016-06-01

    Full Text Available Simple cell-cell interactions can give rise to complex cellular patterns. For example, neurons of the same type can interact to create a complex patchwork of non-overlapping dendrite arbors, a pattern known as dendrite tiling. Dendrite tiling often involves mutual repulsion between neighboring neurons. While dendrite tiling is found across nervous systems, the nematode Caenorhabditis elegans has a relatively simple nervous system with few opportunities for tiling. Here, we show that genetic duplication of a single neuron, PVD, is sufficient to create dendrite tiling among the resulting ectopic neurons. We use laser ablation to show that this tiling is mediated by mutual repulsion between neighbors. Furthermore, we find that tiling requires a repulsion signal (UNC-6/Netrin and its receptors UNC-40/DCC and UNC-5 that normally patterns the PVD dendrite arbor. These results demonstrate that an apparently complex cellular pattern can emerge in a simple nervous system merely by increasing neuron number.

  16. Insight into the three-dimensional structure of maize chlorotic mottle virus revealed by Cryo-EM single particle analysis.

    Science.gov (United States)

    Wang, Chun-Yan; Zhang, Qin-Fen; Gao, Yuan-Zhu; Zhou, Xue-Ping; Ji, Gang; Huang, Xiao-Jun; Hong, Jian; Zhang, Chuan-Xi

    2015-11-01

    Maize chlorotic mottle virus (MCMV) is the only member of the Machlomovirus genus in the family Tombusviridae. Here, we obtained the Cryo-EM structure of MCMV by single particle analysis with most local resolution at approximately 4 Å. The Cα backbone was built based on residues with bulky side chains. The resolved C-terminus of the capsid protein subunit and obvious openings at the 2-fold axis demonstrated the compactness of the asymmetric unit, which indicates an important role in the stability of MCMV. The Asp116 residue from each subunit around the 5-fold and 3-fold axes contributed to the negative charges in the centers of the pentamers and hexamers, which might serve as a solid barrier against the leakage of genomic RNA. Finally, the loops most exposed on the surface were analyzed and are proposed to be potential functional sites related to MCMV transmission.

  17. Structure-based molecular simulations reveal the enhancement of biased Brownian motions in single-headed kinesin.

    Directory of Open Access Journals (Sweden)

    Ryo Kanada

    Full Text Available Kinesin is a family of molecular motors that move unidirectionally along microtubules (MT using ATP hydrolysis free energy. In the family, the conventional two-headed kinesin was experimentally characterized to move unidirectionally through "walking" in a hand-over-hand fashion by coordinated motions of the two heads. Interestingly a single-headed kinesin, a truncated KIF1A, still can generate a biased Brownian movement along MT, as observed by in vitro single molecule experiments. Thus, KIF1A must use a different mechanism from the conventional kinesin to achieve the unidirectional motions. Based on the energy landscape view of proteins, for the first time, we conducted a set of molecular simulations of the truncated KIF1A movements over an ATP hydrolysis cycle and found a mechanism exhibiting and enhancing stochastic forward-biased movements in a similar way to those in experiments. First, simulating stand-alone KIF1A, we did not find any biased movements, while we found that KIF1A with a large friction cargo-analog attached to the C-terminus can generate clearly biased Brownian movements upon an ATP hydrolysis cycle. The linked cargo-analog enhanced the detachment of the KIF1A from MT. Once detached, diffusion of the KIF1A head was restricted around the large cargo which was located in front of the head at the time of detachment, thus generating a forward bias of the diffusion. The cargo plays the role of a diffusional anchor, or cane, in KIF1A "walking."

  18. Single-cell genomics reveals features of a Colwellia species that was dominant during the Deepwater Horizon oil spill

    Directory of Open Access Journals (Sweden)

    Olivia eMason

    2014-07-01

    Full Text Available During the Deepwater Horizon (DWH oil spill in the Gulf of Mexico a deep-sea hydrocarbon plume developed resulting in a rapid succession of bacteria. Colwellia eventually supplanted Oceanospirillales, which dominated the plume early in the spill. These successional changes may have resulted, in part, from the changing composition and abundance of hydrocarbons over time. Colwellia abundance peaked when gaseous and simple aromatic hydrocarbons increased, yet the metabolic pathway used by Colwellia in hydrocarbon disposition is unknown. Here we used single-cell genomics to gain insights into the genome properties of a Colwellia enriched during the DWH deep-sea plume. A single amplified genome (SAG of a Colwellia cell isolated from a DWH plume, closely related (avg. 98% 16S rRNA gene similarity to other plume Colwellia, was sequenced and annotated. The SAG was similar to the sequenced isolate Colwellia psychrerythraea 34H (84% avg. nucleotide identity. Both had genes for denitrification, chemotaxis and motility, adaptations to cold environments, and a suite of nutrient acquisition genes. The Colwellia SAG may be capable of gaseous and aromatic hydrocarbon degradation, which contrasts with a DWH plume Oceanospirillales SAG genome which encoded non-gaseous n-alkane and cycloalkane degradation. The disparate hydrocarbon degradation pathways are consistent with hydrocarbons that were abundant at different times in the deep-sea plume; first, non-gaseous n-alkanes and cycloalkanes that could be degraded by Oceanospirillales, followed by gaseous, and simple aromatic hydrocarbons that may have been degraded by Colwellia. These insights into the genomic properties of a Colwellia species, which were supported by existing metagenomic sequence data from the plume and DWH contaminated sediments, help further our understanding of the successional changes in the dominant microbial players in the plume over the course of the DWH spill.

  19. Noncanonical compensation of zygotic X transcription in early Drosophila melanogaster development revealed through single-embryo RNA-seq.

    Directory of Open Access Journals (Sweden)

    Susan E Lott

    Full Text Available When Drosophila melanogaster embryos initiate zygotic transcription around mitotic cycle 10, the dose-sensitive expression of specialized genes on the X chromosome triggers a sex-determination cascade that, among other things, compensates for differences in sex chromosome dose by hypertranscribing the single X chromosome in males. However, there is an approximately 1 hour delay between the onset of zygotic transcription and the establishment of canonical dosage compensation near the end of mitotic cycle 14. During this time, zygotic transcription drives segmentation, cellularization, and other important developmental events. Since many of the genes involved in these processes are on the X chromosome, we wondered whether they are transcribed at higher levels in females and whether this might lead to sex-specific early embryonic patterning. To investigate this possibility, we developed methods to precisely stage, sex, and characterize the transcriptomes of individual embryos. We measured genome-wide mRNA abundance in male and female embryos at eight timepoints, spanning mitotic cycle 10 through late cycle 14, using polymorphisms between parental lines to distinguish maternal and zygotic transcription. We found limited sex-specific zygotic transcription, with a weak tendency for genes on the X to be expressed at higher levels in females. However, transcripts derived from the single X chromosome in males were more abundant that those derived from either X chromosome in females, demonstrating that there is widespread dosage compensation prior to the activation of the canonical MSL-mediated dosage compensation system. Crucially, this new system of early zygotic dosage compensation results in nearly identical transcript levels for key X-linked developmental regulators, including giant (gt, brinker (brk, buttonhead (btd, and short gastrulation (sog, in male and female embryos.

  20. Phase separation in single In(x)Ga(1-x)N nanowires revealed through a hard X-ray synchrotron nanoprobe.

    Science.gov (United States)

    Segura-Ruiz, J; Martínez-Criado, G; Denker, C; Malindretos, J; Rizzi, A

    2014-03-12

    In this work, we report on the composition, short- and long-range structural order of single molecular beam epitaxy grown In(x)Ga(1-x)N nanowires using a hard X-ray synchrotron nanoprobe. Nano-X-ray fluorescence mapping reveals an axial and radial heterogeneous elemental distribution in the single wires with Ga accumulation at their bottom and outer regions. Polarization-dependent nano-X-ray absorption near edge structure demonstrates that despite the elemental modulation, the tetrahedral order around the Ga atoms remains along the nanowires. Nano-X-ray diffraction mapping on single nanowires shows the existence of at least three different phases at their bottom: an In-poor shell and two In-rich phases. The alloy homogenizes toward the top of the wires, where a single In-rich phase is observed. No signatures of In-metallic precipitates are observed in the diffraction spectra. The In-content along the single nanowires estimated from X-ray fluorescence and diffraction data are in good agreement. A rough picture of these phenomena is briefly presented. We anticipate that this methodology will contribute to a greater understanding of the underlying growth concepts not only of nanowires but also of many nanostructures in materials science.

  1. Emittance Adapter for a Diffraction Limited Synchrotron Radiation Source

    Energy Technology Data Exchange (ETDEWEB)

    Chao, Alexander Wu; /SLAC; Raimondi, Pantaleo; /Frascati

    2012-03-01

    We investigate the possibility of reaching very small horizontal and vertical emittances inside an undulator in a storage ring, by means of a local exchange of the apparent horizontal and vertical emittances, performed with a combination of skew quadrupoles and one solenoid in a dedicated insertion line in the storage ring. The insertion leaves the ring parameters and its optical properties unaffected. This scheme could greatly relax the emittance requirements for a diffraction limited synchrotron light source. The lattice derivation and design is described.

  2. Design of a minimum emittance nBA lattice

    Science.gov (United States)

    Lee, S. Y.

    1998-04-01

    An attempt to design a minimum emittance n-bend achromat (nBA) lattice has been made. One distinct feature is that dipoles with two different lengths were used. As a multiple bend achromat, five bend achromat lattices with six superperiod were designed. The obtained emittace is three times larger than the theoretical minimum. Tunes were chosen to avoid third order resonances. In order to correct first and second order chromaticities, eight family sextupoles were placed. The obtained emittance of five bend achromat lattices is almost equal to the minimum emittance of five bend achromat lattice consisting of dipoles with equal length.

  3. Emittance Compensation in a Flat Beam RF Photoinjector

    Science.gov (United States)

    Rosenzweig, J. B.; Anderson, S.; Colby, E.; Serafini, L.

    1997-05-01

    The beam dynamics of a flat beam rf photoinjector, which is intended to produce asymmetric emittances for linear collider applications, are analyzed, by both analytical and computational methods. The analytical model is a generalization of the recently developed theory of emittance compensation in round beams(L.Serafini, and J.B. Rosenzweig, submitted to Physical Review E.), in which a new mode of laminar flow beam dynamics, the invariant envelope, is found to give the ideal conditions for emittance minimization. Three-dimensional rf and beam dynamics simulations are used to iluminate the analytical results. abstract.

  4. New Low Emittance Lattice for the Super-B Accelerator

    Energy Technology Data Exchange (ETDEWEB)

    Biagini, M.E.; Boscolo, M.; Raimondi, P.; Tomassini, S.; Zobov, M.; /Frascati; Seeman, J.; Sullivan, M.; Wienands, U.; Wittmer, W.; /SLAC; Bettoni, S.; /CERN; Paoloni, E.; /Pisa U. /INFN, Pisa; Bogomyagkov, A.; Koop, I.; Levichev, E.; Nikitin, S.; Piminov, P.; Shatilov, D.; /Novosibirsk, IYF

    2011-10-21

    New low emittance lattices have been designed for the asymmetric SuperB accelerator, aiming at a luminosity of 10{sup 36} cm{sup -2} s{sup -1}. Main optics features are two alternating arc cells with different horizontal phase advance, decreasing beam emittance and allowing at the same time for easy chromaticity correction in the arcs. Emittance can be further reduced by a factor of two for luminosity upgrade. Spin rotation schemes for the e{sup -} beam have been studied to provide longitudinal polarization at the IP, and implementation into the lattice is in progress.

  5. Observation of picometer vertical emittance with a vertical undulator.

    Science.gov (United States)

    Wootton, K P; Boland, M J; Dowd, R; Tan, Y-R E; Cowie, B C C; Papaphilippou, Y; Taylor, G N; Rassool, R P

    2012-11-09

    Using a vertical undulator, picometer vertical electron beam emittances have been observed at the Australian Synchrotron storage ring. An APPLE-II type undulator was phased to produce a horizontal magnetic field, which creates a synchrotron radiation field that is very sensitive to the vertical electron beam emittance. The measured ratios of undulator spectral peak heights are evaluated by fitting to simulations of the apparatus. With this apparatus immediately available at most existing electron and positron storage rings, we find this to be an appropriate and novel vertical emittance diagnostic.

  6. Direct Observation of Ultralow Vertical Emittance using a Vertical Undulator

    Energy Technology Data Exchange (ETDEWEB)

    Wootton, Kent

    2015-09-17

    In recent work, the first quantitative measurements of electron beam vertical emittance using a vertical undulator were presented, with particular emphasis given to ultralow vertical emittances [K. P. Wootton, et al., Phys. Rev. ST Accel. Beams, 17, 112802 (2014)]. Using this apparatus, a geometric vertical emittance of 0.9 ± 0.3 pm rad has been observed. A critical analysis is given of measurement approaches that were attempted, with particular emphasis on systematic and statistical uncertainties. The method used is explained, compared to other techniques and the applicability of these results to other scenarios discussed.

  7. Single-cell duplex RT-LATE-PCR reveals Oct4 and Xist RNA gradients in 8-cell embryos

    Directory of Open Access Journals (Sweden)

    Hartung Odelya

    2007-12-01

    Full Text Available Abstract Background The formation of two distinctive cell lineages in preimplantation mouse embryos is characterized by differential gene expression. The cells of the inner cell mass are pluripotent and express high levels of Oct4 mRNA, which is down-regulated in the surrounding trophectoderm. In contrast, the trophectoderm of female embryos contains Xist mRNA, which is absent from cells of the inner mass. Prior to blastocyst formation, all blastomeres of female embryos still express both of these RNAs. We, thus, postulated that simultaneous quantification of Oct4 and Xist transcripts in individual blastomeres at the 8-cell stage could be informative as to their subsequent fate. Testing this hypothesis, however, presented numerous technical challenges. We overcame these difficulties by combining PurAmp, a single-tube method for RNA preparation and quantification, with LATE-PCR, an advanced form of asymmetric PCR. Results We constructed a duplex RT-LATE-PCR assay for real-time measurement of Oct4 and Xist templates and confirmed its specificity and quantitative accuracy with different methods. We then undertook analysis of sets of blastomeres isolated from embryos at the 8-cell stage. At this stage, all cells in the embryo are still pluripotent and morphologically equivalent. Our results demonstrate, however, that both Oct4 and Xist RNA levels vary in individual blastomeres comprising the same embryo, with some cells having particularly elevated levels of either transcript. Analysis of multiple embryos also shows that Xist and Oct4 expression levels are not correlated at the 8-cell stage, although transcription of both genes is up-regulated at this time in development. In addition, comparison of data from males and females allowed us to determine that the efficiency of the Oct4/Xist assay is unaffected by sex-related differences in gene expression. Conclusion This paper describes the first example of multiplex RT-LATE-PCR and its utility, when

  8. Conformational transition of FGFR kinase activation revealed by site-specific unnatural amino acid reporter and single molecule FRET

    Science.gov (United States)

    Perdios, Louis; Lowe, Alan R.; Saladino, Giorgio; Bunney, Tom D.; Thiyagarajan, Nethaji; Alexandrov, Yuriy; Dunsby, Christopher; French, Paul M. W.; Chin, Jason W.; Gervasio, Francesco Luigi; Tate, Edward W.; Katan, Matilda

    2017-01-01

    Protein kinases share significant structural similarity; however, structural features alone are insufficient to explain their diverse functions. Thus, bridging the gap between static structure and function requires a more detailed understanding of their dynamic properties. For example, kinase activation may occur via a switch-like mechanism or by shifting a dynamic equilibrium between inactive and active states. Here, we utilize a combination of FRET and molecular dynamics (MD) simulations to probe the activation mechanism of the kinase domain of Fibroblast Growth Factor Receptor (FGFR). Using genetically-encoded, site-specific incorporation of unnatural amino acids in regions essential for activation, followed by specific labeling with fluorescent moieties, we generated a novel class of FRET-based reporter to monitor conformational differences corresponding to states sampled by non phosphorylated/inactive and phosphorylated/active forms of the kinase. Single molecule FRET analysis in vitro, combined with MD simulations, shows that for FGFR kinase, there are populations of inactive and active states separated by a high free energy barrier resulting in switch-like activation. Compared to recent studies, these findings support diversity in features of kinases that impact on their activation mechanisms. The properties of these FRET-based constructs will also allow further studies of kinase dynamics as well as applications in vivo.

  9. Single-strand conformation polymorphism-based analysis reveals genetic variation within Spirometra erinacei (Cestoda: Pseudophyllidea) from Australia.

    Science.gov (United States)

    Zhu, X Q; Beveridge, I; Berger, L; Barton, D; Gasser, R B

    2002-04-01

    This study examined genetic variability within Spirometra erinacei (Cestoda: Pseudophyllidea) from different host species and geographical origins in Australia using a polymerase chain reaction (PCR)-based mutation detection approach, followed by DNA sequencing. Part of the cytochrome c oxidase subunit 1 gene (p cox 1) was amplified by PCR, scanned for sequence variation by single-strand conformation polymorphism (SSCP), and representative samples from different host species were selected for DNA sequencing. While no variation in SSCP profiles was detected among S. erinacei samples from dog, fox, cat, tiger snake and python, they differed in profile from 5 specimens from the green tree frog (Litoria caerulea). This was supported by sequence data which demonstrated that p cox 1 sequences of samples from the latter host species differed at 8 of 393 (2%) nucleotide positions from those from the non-amphibian host. Using a nucleotide difference in the p cox 1 sequence, a PCR-linked restriction fragment length polymorphism (RFLP) could be employed to unequivocally delineate between samples from non-amphibian and amphibian hosts. These findings demonstrate the existence of at least two genotypes within S. erinacei, which may have important implications for studying the epidemiology, ecology and systematics of this cestode.

  10. Ear manipulations reveal a critical period for survival and dendritic development at the single-cell level in Mauthner neurons.

    Science.gov (United States)

    Elliott, Karen L; Houston, Douglas W; DeCook, Rhonda; Fritzsch, Bernd

    2015-12-01

    Second-order sensory neurons are dependent on afferents from the sense organs during a critical period in development for their survival and differentiation. Past research has mostly focused on whole populations of neurons, hampering progress in understanding the mechanisms underlying these critical phases. To move toward a better understanding of the molecular and cellular basis of afferent-dependent neuronal development, we developed a new model to study the effects of ear removal on a single identifiable cell in the hindbrain of a frog, the Mauthner cell. Ear extirpation at various stages of Xenopus laevis development defines a critical period of progressively-reduced dependency of Mauthner cell survival/differentiation on the ear afferents. Furthermore, ear removal results in a progressively decreased reduction in the number of dendritic branches. Conversely, addition of an ear results in an increase in the number of dendritic branches. These results suggest that the duration of innervation and the number of inner ear afferents play a quantitative role in Mauthner cell survival/differentiation, including dendritic development.

  11. Raman spectroscopy of individual monocytes reveals that single-beam optical trapping of mononuclear cells occurs by their nucleus

    Science.gov (United States)

    Fore, Samantha; Chan, James; Taylor, Douglas; Huser, Thomas

    2011-01-01

    We show that laser-tweezers Raman spectroscopy of eukaryotic cells with a significantly larger diameter than the tight focus of a single beam laser trap leads to optical trapping of the cell by its optically densest part, i.e. typically the cell’s nucleus. Raman spectra of individual optically trapped monocytes are compared with location-specific Raman spectra of monocytes adhered to a substrate. When the cell’s nucleus is stained with a fluorescent live cell stain, the Raman spectrum of the DNA-specific stain is observed only in the nucleus of individual monocytes. Optically trapped monocytes display the same behavior. We also show that the Raman spectra of individual monocytes exhibit the characteristic Raman signature of cells that have not yet fully differentiated and that individual primary monocytes can be distinguished from transformed monocytes based on their Raman spectra. This work provides further evidence that laser tweezers Raman spectroscopy of individual cells provides meaningful biochemical information in an entirely nondestructive fashion that permits discerning differences between cell types and cellular activity. PMID:21984959

  12. Functional characterization of a conserved archaeal viral operon revealing single-stranded DNA binding, annealing and nuclease activities

    DEFF Research Database (Denmark)

    Guo, Yang; Kragelund, Birthe Brandt; White, Malcolm F.

    2015-01-01

    The majority of archaeal viral genes are of unknown function hindering our understanding of the virus life cycle and viral interactions with their host. Here, we first describe functional characterization of ORF131b (gp17) and ORF436 (gp18) of Sulfolobus islandicus rod-shaped virus 2 (SIRV2), bot...... for rudiviruses and the close interaction among the ssDNA binding, annealing and nuclease proteins strongly point to a role of the gene operon in genome maturation and/or DNA recombination that may function in viral DNA replication/repair.......The majority of archaeal viral genes are of unknown function hindering our understanding of the virus life cycle and viral interactions with their host. Here, we first describe functional characterization of ORF131b (gp17) and ORF436 (gp18) of Sulfolobus islandicus rod-shaped virus 2 (SIRV2), both...... encoding proteins of unknown function and forming an operon with ORF207 (gp19). SIRV2 gp17 was found to be a single-stranded DNA (ssDNA) binding protein different in structure from all previously characterized ssDNA binding proteins. Mutagenesis of a few conserved basic residues suggested a U...

  13. Cells Respond to Distinct Nanoparticle Properties with Multiple Strategies As Revealed by Single-Cell RNA-Seq

    Energy Technology Data Exchange (ETDEWEB)

    Mitchell, Hugh D.; Markillie, Lye Meng; Chrisler, William B.; Gaffrey, Matthew J.; Hu, Dehong; Szymanski, Craig J.; Xie, Yumei; Melby, Eric S.; Dohnalkova, Alice; Taylor, Ronald C.; Grate, Eva K.; Cooley, Scott K.; McDermott, Jason E.; Heredia-Langner, Alejandro; Orr, Galya

    2016-11-22

    The impact of distinct nanoparticle (NP) properties on cellular response and ultimately human health is unclear. This gap is partially due to experimental difficulties in achieving uniform NP loads in the studied cells, creating heterogeneous populations with some cells “overloaded” while other cells are loaded with few or no NPs. Yet gene expression studies have been conducted in the population as a whole, identifying generic responses, while missing unique responses due to signal averaging across many cells, each carrying different loads. Here we applied single-cell RNA-Seq to alveolar epithelial cells carrying defined loads of aminated or carboxylated quantum dots (QDs), showing higher or lower toxicity, respectively. Interestingly, cells carrying lower loads responded with multiple strategies, mostly with upregulated processes, which were nonetheless coherent and unique to each QD type. In contrast, cells carrying higher loads responded more uniformly, with mostly downregulated processes that were shared across QD types. Strategies unique to aminated QDs showed strong upregulation of stress responses, coupled in some cases with regulation of cell cycle, protein synthesis and organelle activities. In contrast, strategies unique to carboxylated QDs showed upregulation of DNA repair and RNA activities, and decreased regulation of cell division, coupled in some cases with upregulation of stress responses and ATP related functions. Together, our studies suggest scenarios where higher NP loads lock cells into uniform responses, mostly shutdown of cellular processes, whereas lower loads allow for unique responses to each NP type that are more diversified, proactive defenses or repairs of the NP insults.

  14. Single-Cell RNAseq Reveals That Pancreatic β-Cells From Very Old Male Mice Have a Young Gene Signature.

    Science.gov (United States)

    Xin, Yurong; Okamoto, Haruka; Kim, Jinrang; Ni, Min; Adler, Christina; Cavino, Katie; Na, Erqian; Murphy, Andrew J; Yancopoulos, George D; Lin, Calvin; Gromada, Jesper

    2016-09-01

    Aging improves pancreatic β-cell function in mice. This is a surprising finding because aging is typically associated with functional decline. We performed single-cell RNA sequencing of β-cells from 3- and 26-month-old mice to explore how changes in gene expression contribute to improved function with age. The old mice were healthy and had reduced blood glucose levels and increased β-cell mass, which correlated to their body weight. β-Cells from young and old mice had similar transcriptome profiles. In fact, only 193 genes (0.89% of all detected genes) were significantly regulated (≥2-fold; false discovery rate 5). Of these, 183 were down-regulated and mainly associated with pathways regulating gene expression, cell cycle, cell death, and survival as well as cellular movement, function, and maintenance. Collectively our data show that β-cells from very old mice have transcriptome profiles similar to those of young mice. These data support previous findings that aging is not associated with reduced β-cell mass or functional β-cell decline in mice.

  15. Mechanisms for Improved Hygroscopicity of L-Arginine Valproate Revealed by X-Ray Single Crystal Structure Analysis.

    Science.gov (United States)

    Ito, Masataka; Nambu, Kaori; Sakon, Aya; Uekusa, Hidehiro; Yonemochi, Etsuo; Noguchi, Shuji; Terada, Katsuhide

    2017-03-01

    Valproic acid is widely used as an antiepileptic agent. Valproic acid is in liquid phase while sodium valproate is in solid phase at room temperature. Sodium valproate is hard to manufacture because of its hygroscopic and deliquescent properties. To improve these, cocrystal and salt screening for valproic acid was employed in this study. Two solid salt forms, l-arginine valproate and l-lysine valproate, were obtained and characterized. By using dynamic vapor sorption method, the critical relative humidity of sodium valproate, l-arginine valproate, and l-lysine valproate were measured. Critical relative humidity of sodium valproate was 40%, of l-lysine valproate was 60%, and of l-arginine valproate was 70%. Single-crystal X-ray structure determination of l-arginine valproate was employed. l-Lysine valproate was of low diffraction quality, and l-arginine valproate formed a 1:1 salt. Crystal l-arginine valproate has a disorder in the methylene carbon chain that creates 2 conformations. The carboxylate group of valproic acid is connected to the amino group of l-arginine. Crystalline morphologies were calculated from its crystal structure. Adsorption of water molecules to crystal facets was simulated by Material Studio. When comparing adsorption energy per site of these salts, sodium valproate is more capable of adsorption of water molecule than l-arginine valproate.

  16. Deep RNA sequencing reveals the smallest known mitochondrial micro exon in animals: The placozoan cox1 single base pair exon.

    Science.gov (United States)

    Osigus, Hans-Jürgen; Eitel, Michael; Schierwater, Bernd

    2017-01-01

    The phylum Placozoa holds a key position for our understanding of the evolution of mitochondrial genomes in Metazoa. Placozoans possess large mitochondrial genomes which harbor several remarkable characteristics such as a fragmented cox1 gene and trans-splicing cox1 introns. A previous study also suggested the existence of cox1 mRNA editing in Trichoplax adhaerens, yet the only formally described species in the phylum Placozoa. We have analyzed RNA-seq data of the undescribed sister species, Placozoa sp. H2 ("Panama" clone), with special focus on the mitochondrial mRNA. While we did not find support for a previously postulated cox1 mRNA editing mechanism, we surprisingly found two independent transcripts representing intermediate cox1 mRNA splicing stages. Both transcripts consist of partial cox1 exon as well as overlapping intron fragments. The data suggest that the cox1 gene harbors a single base pair (cytosine) micro exon. Furthermore, conserved group I intron structures flank this unique micro exon also in other placozoans. We discuss the evolutionary origin of this micro exon in the context of a self-splicing intron gain in the cox1 gene of the last common ancestor of extant placozoans.

  17. Conformational transition of FGFR kinase activation revealed by site-specific unnatural amino acid reporter and single molecule FRET

    Science.gov (United States)

    Perdios, Louis; Lowe, Alan R.; Saladino, Giorgio; Bunney, Tom D.; Thiyagarajan, Nethaji; Alexandrov, Yuriy; Dunsby, Christopher; French, Paul M. W.; Chin, Jason W.; Gervasio, Francesco Luigi; Tate, Edward W.; Katan, Matilda

    2017-01-01

    Protein kinases share significant structural similarity; however, structural features alone are insufficient to explain their diverse functions. Thus, bridging the gap between static structure and function requires a more detailed understanding of their dynamic properties. For example, kinase activation may occur via a switch-like mechanism or by shifting a dynamic equilibrium between inactive and active states. Here, we utilize a combination of FRET and molecular dynamics (MD) simulations to probe the activation mechanism of the kinase domain of Fibroblast Growth Factor Receptor (FGFR). Using genetically-encoded, site-specific incorporation of unnatural amino acids in regions essential for activation, followed by specific labeling with fluorescent moieties, we generated a novel class of FRET-based reporter to monitor conformational differences corresponding to states sampled by non phosphorylated/inactive and phosphorylated/active forms of the kinase. Single molecule FRET analysis in vitro, combined with MD simulations, shows that for FGFR kinase, there are populations of inactive and active states separated by a high free energy barrier resulting in switch-like activation. Compared to recent studies, these findings support diversity in features of kinases that impact on their activation mechanisms. The properties of these FRET-based constructs will also allow further studies of kinase dynamics as well as applications in vivo. PMID:28045057

  18. Confined Diffusion Without Fences of a G-Protein-Coupled Receptor as Revealed by Single Particle Tracking

    Science.gov (United States)

    Daumas, Frédéric; Destainville, Nicolas; Millot, Claire; Lopez, André; Dean, David; Salomé, Laurence

    2003-01-01

    Single particle tracking is a powerful tool for probing the organization and dynamics of the plasma membrane constituents. We used this technique to study the μ-opioid receptor belonging to the large family of the G-protein-coupled receptors involved with other partners in a signal transduction pathway. The specific labeling of the receptor coupled to a T7-tag at its N-terminus, stably expressed in fibroblastic cells, was achieved by colloidal gold coupled to a monoclonal anti T7-tag antibody. The lateral movements of the particles were followed by nanovideomicroscopy at 40 ms time resolution during 2 min with a spatial precision of 15 nm. The receptors were found to have either a slow or directed diffusion mode (10%) or a walking confined diffusion mode (90%) composed of a long-term random diffusion and a short-term confined diffusion, and corresponding to a diffusion confined within a domain that itself diffuses. The results indicate that the confinement is due to an effective harmonic potential generated by long-range attraction between the membrane proteins. A simple model for interacting membrane proteins diffusion is proposed that explains the variations with the domain size of the short-term and long-term diffusion coefficients. PMID:12524289

  19. Specific-Locus Amplified Fragment Sequencing Reveals Spontaneous Single-Nucleotide Mutations in Rice OsMsh6 Mutants

    Directory of Open Access Journals (Sweden)

    Hairui Cui

    2017-01-01

    Full Text Available Genomic stability depends in part on an efficient DNA lesion recognition and correction by the DNA mismatch repair (MMR system. We investigated mutations arising spontaneously in rice OsMsh6 mutants by specific-locus amplified fragment sequencing. Totally 994 single-nucleotide mutations were identified in three mutants and on average the mutation density is about 1/136.72 Kb per mutant line. These mutations were relatively randomly distributed in genome and might be accumulated in generation-dependent manner. All possible base transitions and base transversions could be seen and the ratio of transitions to transversions was about 3.12. We also observed the nearest-neighbor bias around the mutated base. Our data suggests that OsMsh6 (LOC_Os09g24220 is important in ensuring genome stability by recognizing mismatches that arise spontaneously and provides useful information for investigating the function of the OsMsh6 gene in DNA repair and exploiting MMR mutants in rice induced mutation breeding.

  20. Collinear antiferromagnetism in trigonal SrMn2As2 revealed by single-crystal neutron diffraction

    Science.gov (United States)

    Das, Pinaki; Sangeetha, N. S.; Pandey, Abhishek; Benson, Zackery A.; Heitmann, T. W.; Johnston, D. C.; Goldman, A. I.; Kreyssig, A.

    2017-01-01

    Iron pnictides and related materials have been a topic of intense research for understanding the complex interplay between magnetism and superconductivity. Here we report on the magnetic structure of SrMn2As2 that crystallizes in a trigonal structure (P\\bar{3}m1 ) and undergoes an antiferromagnetic (AFM) transition at {{T}\\text{N}}=118(2) K. The magnetic susceptibility remains nearly constant at temperatures T≤slant {{T}\\text{N}} with \\boldsymbol{H}\\parallel \\boldsymbol{c} whereas it decreases significantly with \\boldsymbol{H}\\parallel \\boldsymbol{a}\\boldsymbol{b} . This shows that the ordered Mn moments lie in the \\boldsymbol{a}\\boldsymbol{b} plane instead of aligning along the \\boldsymbol{c} -axis as in tetragonal BaMn2As2. Single-crystal neutron diffraction measurements on SrMn2As2 demonstrate that the Mn moments are ordered in a collinear Néel AFM phase with {{180}\\circ} AFM alignment between a moment and all nearest neighbor moments in the basal plane and also perpendicular to it. Moreover, quasi-two-dimensional AFM order is manifested in SrMn2As2 as evident from the temperature dependence of the order parameter.

  1. Single-molecule imaging of Nav1.6 on the somatic surface of hippocampal neurons reveals unique nanoclusters

    CERN Document Server

    Akin, Elizabeth J; Johnson, Ben; Beheiry, Mohamed el; Masson, Jean-Baptiste; Krapf, Diego; Tamkun, Michael M

    2016-01-01

    Voltage-gated sodium (Na$_v$) channels are responsible for the depolarizing phase of the action potential in most nerve cells and Na$_v$ channel localization to the axon initial segment is vital to action potential initiation. Na$_v$ channels in the soma play a role in the transfer of axonal output information to the rest of the neuron and in synaptic plasticity, although little is known about Na$_v$ channel localization and dynamics within this neuronal compartment. The present study uses single-particle tracking and photoactivation localization microscopy to analyze cell-surface Na$_v$1.6 within the soma of cultured hippocampal neurons. Mean square displacement analysis of individual trajectories indicated half of the somatic Na$_v$1.6 channels localized to stable nanoclusters ~230 nm in diameter. Strikingly, these domains were stabilized at specific sites on the cell membrane for greater than 30 min, notably via an ankyrin-independent mechanism, indicating the mechanism by which Na$_v$1.6 nanoclusters are ...

  2. Single-cell transcriptomes identify human islet cell signatures and reveal cell-type–specific expression changes in type 2 diabetes

    Science.gov (United States)

    Bolisetty, Mohan; Kursawe, Romy; Sun, Lili; Sivakamasundari, V.; Kycia, Ina

    2017-01-01

    Blood glucose levels are tightly controlled by the coordinated action of at least four cell types constituting pancreatic islets. Changes in the proportion and/or function of these cells are associated with genetic and molecular pathophysiology of monogenic, type 1, and type 2 (T2D) diabetes. Cellular heterogeneity impedes precise understanding of the molecular components of each islet cell type that govern islet (dys)function, particularly the less abundant delta and gamma/pancreatic polypeptide (PP) cells. Here, we report single-cell transcriptomes for 638 cells from nondiabetic (ND) and T2D human islet samples. Analyses of ND single-cell transcriptomes identified distinct alpha, beta, delta, and PP/gamma cell-type signatures. Genes linked to rare and common forms of islet dysfunction and diabetes were expressed in the delta and PP/gamma cell types. Moreover, this study revealed that delta cells specifically express receptors that receive and coordinate systemic cues from the leptin, ghrelin, and dopamine signaling pathways implicating them as integrators of central and peripheral metabolic signals into the pancreatic islet. Finally, single-cell transcriptome profiling revealed genes differentially regulated between T2D and ND alpha, beta, and delta cells that were undetectable in paired whole islet analyses. This study thus identifies fundamental cell-type–specific features of pancreatic islet (dys)function and provides a critical resource for comprehensive understanding of islet biology and diabetes pathogenesis. PMID:27864352

  3. Revealing mechanism responsible for structural reversibility of single-crystal VO2 nanorods upon lithiation/delithiation

    Energy Technology Data Exchange (ETDEWEB)

    Liu, Qi; Tan, Guoqiang; Wang, Peng; Abeyweera, Sasitha C.; Zhang, Dongtang; Rong, Yangchun; Wu, Yimin; Lu, Jun; Sun, Cheng-Jun; Ren, Yang; Liu, Yuzi; Muehleisen, Ralph T.; Guzowski, Leah B.; Li, Jie; Xiao, Xianghui; Sun, Yugang

    2017-04-17

    A pure phase of VO2(B) nanorods have been synthesized through an energy-efficient microwave hydrothermal reaction and used as cathode materials of lithium ion batteries, which exhibit promising specific capacity (e.g., 130 mA h g-1 even after 100 charge/discharge cycles) and rate capacity (e.g., ~130 mA h g-1 at a high current of 400 mA g-1). The excellent cyclability originates from the structural reversibility of VO2(B) upon lithiation/delithiation that is confirmed by the in situ high-energy synchrotron X-ray diffraction (HEXRD) and in situ x-ray adsorption near-edge spectroscopy (XANES) of the VO2 nanorods in operating battery cells. As a result, the real-time results reveal that discharge forces lithium ions to insert firstly into the tunnels with the largest size along b direction followed by the second largest tunnels along c direction, which is completely reversible in the charge process.

  4. Prognostic value of cortically induced motor evoked activity by TMS in chronic stroke: Caveats from a revealing single clinical case

    Directory of Open Access Journals (Sweden)

    Amengual Julià L

    2012-06-01

    Full Text Available Abstract Background We report the case of a chronic stroke patient (62 months after injury showing total absence of motor activity evoked by transcranial magnetic stimulation (TMS of spared regions of the left motor cortex, but near-to-complete recovery of motor abilities in the affected hand. Case presentation Multimodal investigations included detailed TMS based motor mapping, motor evoked potentials (MEP, and Cortical Silent period (CSP as well as functional magnetic resonance imaging (fMRI of motor activity, MRI based lesion analysis and Diffusion Tensor Imaging (DTI Tractography of corticospinal tract (CST. Anatomical analysis revealed a left hemisphere subinsular lesion interrupting the descending left CST at the level of the internal capsule. The absence of MEPs after intense TMS pulses to the ipsilesional M1, and the reversible suppression of ongoing electromyographic (EMG activity (indexed by CSP demonstrate a weak modulation of subcortical systems by the ipsilesional left frontal cortex, but an inability to induce efficient descending volleys from those cortical locations to right hand and forearm muscles. Functional MRI recordings under grasping and finger tapping patterns involving the affected hand showed slight signs of subcortical recruitment, as compared to the unaffected hand and hemisphere, as well as the expected cortical activations. Conclusions The potential sources of motor voluntary activity for the affected hand in absence of MEPs are discussed. We conclude that multimodal analysis may contribute to a more accurate prognosis of stroke patients.

  5. Complex organizational structure of the genome revealed by genome-wide analysis of single and alternative promoters in Drosophila melanogaster

    Directory of Open Access Journals (Sweden)

    Zhu Qianqian

    2009-01-01

    Full Text Available Abstract Background The promoter is a critical necessary transcriptional cis-regulatory element. In addition to its role as an assembly site for the basal transcriptional apparatus, the promoter plays a key part in mediating temporal and spatial aspects of gene expression through differential binding of transcription factors and selective interaction with distal enhancers. Although many genes have multiple promoters, little attention has been focused on how these relate to one another; nor has much study been directed at relationships between promoters of adjacent genes. Results We have undertaken a systematic investigation of Drosophila promoters. We divided promoters into three groups: unique promoters, first alternative promoters (the most 5' of a gene's multiple promoters, and downstream alternative promoters (the remaining alternative promoters 3' to the first. We observed distinct nucleotide distribution and sequence motif preferences among these three classes. We also investigated the promoters of neighboring genes and found that a greater than expected number of adjacent genes have similar sequence motif profiles, which may allow the genes to be regulated in a coordinated fashion. Consistent with this, there is a positive correlation between similar promoter motifs and related gene expression profiles for these genes. Conclusions Our results suggest that different regulatory mechanisms may apply to each of the three promoter classes, and provide a mechanism for "gene expression neighborhoods," local clusters of co-expressed genes. As a whole, our data reveal an unexpected complexity of genomic organization at the promoter level with respect to both alternative and neighboring promoters.

  6. Deep sequencing of pyrethroid-resistant bed bugs reveals multiple mechanisms of resistance within a single population.

    Science.gov (United States)

    Adelman, Zach N; Kilcullen, Kathleen A; Koganemaru, Reina; Anderson, Michelle A E; Anderson, Troy D; Miller, Dini M

    2011-01-01

    A frightening resurgence of bed bug infestations has occurred over the last 10 years in the U.S. and current chemical methods have been inadequate for controlling this pest due to widespread insecticide resistance. Little is known about the mechanisms of resistance present in U.S. bed bug populations, making it extremely difficult to develop intelligent strategies for their control. We have identified bed bugs collected in Richmond, VA which exhibit both kdr-type (L925I) and metabolic resistance to pyrethroid insecticides. Using LD(50) bioassays, we determined that resistance ratios for Richmond strain bed bugs were ∼5200-fold to the insecticide deltamethrin. To identify metabolic genes potentially involved in the detoxification of pyrethroids, we performed deep-sequencing of the adult bed bug transcriptome, obtaining more than 2.5 million reads on the 454 titanium platform. Following assembly, analysis of newly identified gene transcripts in both Harlan (susceptible) and Richmond (resistant) bed bugs revealed several candidate cytochrome P450 and carboxylesterase genes which were significantly over-expressed in the resistant strain, consistent with the idea of increased metabolic resistance. These data will accelerate efforts to understand the biochemical basis for insecticide resistance in bed bugs, and provide molecular markers to assist in the surveillance of metabolic resistance.

  7. Deep sequencing of pyrethroid-resistant bed bugs reveals multiple mechanisms of resistance within a single population.

    Directory of Open Access Journals (Sweden)

    Zach N Adelman

    Full Text Available A frightening resurgence of bed bug infestations has occurred over the last 10 years in the U.S. and current chemical methods have been inadequate for controlling this pest due to widespread insecticide resistance. Little is known about the mechanisms of resistance present in U.S. bed bug populations, making it extremely difficult to develop intelligent strategies for their control. We have identified bed bugs collected in Richmond, VA which exhibit both kdr-type (L925I and metabolic resistance to pyrethroid insecticides. Using LD(50 bioassays, we determined that resistance ratios for Richmond strain bed bugs were ∼5200-fold to the insecticide deltamethrin. To identify metabolic genes potentially involved in the detoxification of pyrethroids, we performed deep-sequencing of the adult bed bug transcriptome, obtaining more than 2.5 million reads on the 454 titanium platform. Following assembly, analysis of newly identified gene transcripts in both Harlan (susceptible and Richmond (resistant bed bugs revealed several candidate cytochrome P450 and carboxylesterase genes which were significantly over-expressed in the resistant strain, consistent with the idea of increased metabolic resistance. These data will accelerate efforts to understand the biochemical basis for insecticide resistance in bed bugs, and provide molecular markers to assist in the surveillance of metabolic resistance.

  8. Prognostic Value of Cortically Induced Motor Evoked Activity by TMS in Chronic Stroke: Caveats from a Revealing Single Clinical Case

    LENUS (Irish Health Repository)

    Amengual, Julià L

    2012-06-08

    AbstractBackgroundWe report the case of a chronic stroke patient (62 months after injury) showing total absence of motor activity evoked by transcranial magnetic stimulation (TMS) of spared regions of the left motor cortex, but near-to-complete recovery of motor abilities in the affected hand.Case presentationMultimodal investigations included detailed TMS based motor mapping, motor evoked potentials (MEP), and Cortical Silent period (CSP) as well as functional magnetic resonance imaging (fMRI) of motor activity, MRI based lesion analysis and Diffusion Tensor Imaging (DTI) Tractography of corticospinal tract (CST). Anatomical analysis revealed a left hemisphere subinsular lesion interrupting the descending left CST at the level of the internal capsule. The absence of MEPs after intense TMS pulses to the ipsilesional M1, and the reversible suppression of ongoing electromyographic (EMG) activity (indexed by CSP) demonstrate a weak modulation of subcortical systems by the ipsilesional left frontal cortex, but an inability to induce efficient descending volleys from those cortical locations to right hand and forearm muscles. Functional MRI recordings under grasping and finger tapping patterns involving the affected hand showed slight signs of subcortical recruitment, as compared to the unaffected hand and hemisphere, as well as the expected cortical activations.ConclusionsThe potential sources of motor voluntary activity for the affected hand in absence of MEPs are discussed. We conclude that multimodal analysis may contribute to a more accurate prognosis of stroke patients.

  9. Silicon based solar cells using a multilayer oxide as emitter

    Science.gov (United States)

    Bao, Jie; Wu, Weiliang; Liu, Zongtao; Shen, Hui

    2016-08-01

    In this work, n-type silicon based solar cells with WO3/Ag/WO3 multilayer films as emitter (WAW/n-Si solar cells) were presented via simple physical vapor deposition (PVD). Microstructure and composition of WAW/n-Si solar cells were studied by TEM and XPS, respectively. Furthermore, the dependence of the solar cells performances on each WO3 layer thickness was investigated. The results indicated that the bottom WO3 layer mainly induced band bending and facilitated charge-carriers separation, while the top WO3 layer degraded open-circuit voltage but actually improved optical absorption of the solar cells. The WAW/n-Si solar cells, with optimized bottom and top WO3 layer thicknesses, exhibited 5.21% efficiency on polished wafer with area of 4 cm2 under AM 1.5 condition (25 °C and 100 mW/cm2). Compared with WO3 single-layer film, WAW multilayer films demonstrated better surface passivation quality but more optical loss, while the optical loss could be effectively reduced by implementing light-trapping structures. These results pave a new way for dopant-free solar cells in terms of low-cost and facile process flow.

  10. Silicon based solar cells using a multilayer oxide as emitter

    Directory of Open Access Journals (Sweden)

    Jie Bao

    2016-08-01

    Full Text Available In this work, n-type silicon based solar cells with WO3/Ag/WO3 multilayer films as emitter (WAW/n-Si solar cells were presented via simple physical vapor deposition (PVD. Microstructure and composition of WAW/n-Si solar cells were studied by TEM and XPS, respectively. Furthermore, the dependence of the solar cells performances on each WO3 layer thickness was investigated. The results indicated that the bottom WO3 layer mainly induced band bending and facilitated charge-carriers separation, while the top WO3 layer degraded open-circuit voltage but actually improved optical absorption of the solar cells. The WAW/n-Si solar cells, with optimized bottom and top WO3 layer thicknesses, exhibited 5.21% efficiency on polished wafer with area of 4 cm2 under AM 1.5 condition (25 °C and 100 mW/cm2. Compared with WO3 single-layer film, WAW multilayer films demonstrated better surface passivation quality but more optical loss, while the optical loss could be effectively reduced by implementing light-trapping structures. These results pave a new way for dopant-free solar cells in terms of low-cost and facile process flow.

  11. High redshift Lya emitters: clues on the Milky Way infancy

    CERN Document Server

    Salvadori, S; Ferrara, A

    2010-01-01

    With the aim of determining if Milky Way (MW) progenitors could be identified as high redshift Lyman Alpha Emitters (LAEs) we have derived the intrinsic properties of z ~ 5.7 MW progenitors, which are then used to compute their observed Lyman-alpha luminosity, L_alpha, and equivalent width, EW. MW progenitors visible as LAEs are selected according to the canonical observational criterion, L_alpha > 10^42 erg/s and EW > 20 A. Progenitors of MW-like galaxies have L_alpha = 10^(39-43.25) erg/s, making some of them visible as LAEs. In any single MW merger tree realization, typically only 1 (out of ~ 50) progenitor meets the LAE selection criterion, but the probability to have at least one LAE is very high, P = 68%. The identified LAE stars have ages, t_* ~ 150-400 Myr at z ~ 5.7 with the exception of five small progenitors with t_* 10% of the halo very metal-poor stars [Fe/H] < -2, thus establishing a potentially fruitful link between high-z galaxies and the Local Universe.

  12. Single molecule force spectroscopy reveals critical roles of hydrophobic core packing in determining the mechanical stability of protein GB1.

    Science.gov (United States)

    Bu, Tianjia; Wang, Hui-Chuan Eileen; Li, Hongbin

    2012-08-21

    Understanding molecular determinants of protein mechanical stability is important not only for elucidating how elastomeric proteins are designed and functioning in biological systems but also for designing protein building blocks with defined nanomechanical properties for constructing novel biomaterials. GB1 is a small α/β protein and exhibits significant mechanical stability. It is thought that the shear topology of GB1 plays an important role in determining its mechanical stability. Here, we combine single molecule atomic force microscopy and protein engineering techniques to investigate the effect of side chain reduction and hydrophobic core packing on the mechanical stability of GB1. We engineered seven point mutants and carried out mechanical φ-value analysis of the mechanical unfolding of GB1. We found that three mutations, which are across the surfaces of two subdomains that are to be sheared by the applied stretching force, in the hydrophobic core (F30L, Y45L, and F52L) result in significant decrease in mechanical unfolding force of GB1. The mechanical unfolding force of these mutants drop by 50-90 pN compared with wild-type GB1, which unfolds at around 180 pN at a pulling speed of 400 nm/s. These results indicate that hydrophobic core packing plays an important role in determining the mechanical stability of GB1 and suggest that optimizing hydrophobic interactions across the surfaces that are to be sheared will likely be an efficient method to enhance the mechanical stability of GB1 and GB1 homologues.

  13. Single molecule analysis of replicated DNA reveals the usage of multiple KSHV genome regions for latent replication.

    Directory of Open Access Journals (Sweden)

    Subhash C Verma

    2011-11-01

    Full Text Available Kaposi's sarcoma associated herpesvirus (KSHV, an etiologic agent of Kaposi's sarcoma, Body Cavity Based Lymphoma and Multicentric Castleman's Disease, establishes lifelong latency in infected cells. The KSHV genome tethers to the host chromosome with the help of a latency associated nuclear antigen (LANA. Additionally, LANA supports replication of the latent origins within the terminal repeats by recruiting cellular factors. Our previous studies identified and characterized another latent origin, which supported the replication of plasmids ex-vivo without LANA expression in trans. Therefore identification of an additional origin site prompted us to analyze the entire KSHV genome for replication initiation sites using single molecule analysis of replicated DNA (SMARD. Our results showed that replication of DNA can initiate throughout the KSHV genome and the usage of these regions is not conserved in two different KSHV strains investigated. SMARD also showed that the utilization of multiple replication initiation sites occurs across large regions of the genome rather than a specified sequence. The replication origin of the terminal repeats showed only a slight preference for their usage indicating that LANA dependent origin at the terminal repeats (TR plays only a limited role in genome duplication. Furthermore, we performed chromatin immunoprecipitation for ORC2 and MCM3, which are part of the pre-replication initiation complex to determine the genomic sites where these proteins accumulate, to provide further characterization of potential replication initiation sites on the KSHV genome. The ChIP data confirmed accumulation of these pre-RC proteins at multiple genomic sites in a cell cycle dependent manner. Our data also show that both the frequency and the sites of replication initiation vary within the two KSHV genomes studied here, suggesting that initiation of replication is likely to be affected by the genomic context rather than the DNA

  14. Single fiber analyses of glycogen-related proteins reveal their differential association with glycogen in rat skeletal muscle.

    Science.gov (United States)

    Murphy, Robyn M; Xu, Hongyang; Latchman, Heidy; Larkins, Noni T; Gooley, Paul R; Stapleton, David I

    2012-12-01

    To understand how glycogen affects skeletal muscle physiology, we examined enzymes essential for muscle glycogen synthesis and degradation using single fibers from quiescent and stimulated rat skeletal muscle. Presenting a shift in paradigm, we show these proteins are differentially associated with glycogen granules. Protein diffusibility and/or abundance of glycogenin, glycogen branching enzyme (GBE), debranching enzyme (GDE), phosphorylase (GP), and synthase (GS) were examined in fibers isolated from rat fast-twitch extensor digitorum longus (EDL) and slow-twitch soleus (SOL) muscle. GDE and GP proteins were more abundant (~10- to 100-fold) in fibers from EDL compared with SOL muscle. GS and glycogenin proteins were similar between muscles while GBE had an approximately fourfold greater abundance in SOL muscle. Mechanically skinned fibers exposed to physiological buffer for 10 min showed ~70% total pools of GBE and GP were diffusible (nonbound), whereas GDE and GS were considerably less diffusible. Intense in vitro stimulation, sufficient to elicit a ~50% decrease in intracellular glycogen, increased diffusibility of GDE, GP, and GS (~15-60%) and decreased GBE diffusibility (~20%). Amylase treatment, which breaks α-1,4 linkages of glycogen, indicated differential diffusibilities and hence glycogen associations of GDE and GS. Membrane solubilization (1% Triton-X-100) allowed a small additional amount of GDE and GS to diffuse from fibers, suggesting the majority of nonglycogen-associated GDE/GS is associated with myofibrillar/contractile network of muscle rather than membranes. Given differences in enzymes required for glycogen metabolism, the current findings suggest glycogen particles have fiber-type-dependent structures. The greater catabolic potential of glycogen breakdown in fast-twitch fibers may account for different contraction induced rates of glycogen utilization.

  15. Functional characterization of a conserved archaeal viral operon revealing single-stranded DNA binding, annealing and nuclease activities.

    Science.gov (United States)

    Guo, Yang; Kragelund, Birthe B; White, Malcolm F; Peng, Xu

    2015-06-19

    The majority of archaeal viral genes are of unknown function hindering our understanding of the virus life cycle and viral interactions with their host. Here, we first describe functional characterization of ORF131b (gp17) and ORF436 (gp18) of Sulfolobus islandicus rod-shaped virus 2 (SIRV2), both encoding proteins of unknown function and forming an operon with ORF207 (gp19). SIRV2 gp17 was found to be a single-stranded DNA (ssDNA) binding protein different in structure from all previously characterized ssDNA binding proteins. Mutagenesis of a few conserved basic residues suggested a U-shaped binding path for ssDNA. The recombinant gp18 showed an ssDNA annealing activity often associated with helicases and recombinases. To gain insight into the biological role of the entire operon, we characterized SIRV2 gp19 and showed it to possess a 5' → 3' ssDNA exonuclease activity, in addition to the previously demonstrated ssDNA endonuclease activity. Further, in vitro pull-down assay demonstrated interactions between gp17 and gp18 and between gp18 and gp19 with the former being mediated by the intrinsically disordered C-terminus of gp17. The strand-displacement replication mode proposed previously for rudiviruses and the close interaction among the ssDNA binding, annealing and nuclease proteins strongly point to a role of the gene operon in genome maturation and/or DNA recombination that may function in viral DNA replication/repair.

  16. Single-nucleotide polymorphism markers from de-novo assembly of the pomegranate transcriptome reveal germplasm genetic diversity.

    Directory of Open Access Journals (Sweden)

    Ron Ophir

    Full Text Available Pomegranate is a valuable crop that is grown commercially in many parts of the world. Wild species have been reported from India, Turkmenistan and Socotra. Pomegranate fruit has a variety of health-beneficial qualities. However, despite this crop's importance, only moderate effort has been invested in studying its biochemical or physiological properties or in establishing genomic and genetic infrastructures. In this study, we reconstructed a transcriptome from two phenotypically different accessions using 454-GS-FLX Titanium technology. These data were used to explore the functional annotation of 45,187 fully annotated contigs. We further compiled a genetic-variation resource of 7,155 simple-sequence repeats (SSRs and 6,500 single-nucleotide polymorphisms (SNPs. A subset of 480 SNPs was sampled to investigate the genetic structure of the broad pomegranate germplasm collection at the Agricultural Research Organization (ARO, which includes accessions from different geographical areas worldwide. This subset of SNPs was found to be polymorphic, with 10.7% loci with minor allele frequencies of (MAF<0.05. These SNPs were successfully used to classify the ARO pomegranate collection into two major groups of accessions: one from India, China and Iran, composed of mainly unknown country origin and which was more of an admixture than the other major group, composed of accessions mainly from the Mediterranean basin, Central Asia and California. This study establishes a high-throughput transcriptome and genetic-marker infrastructure. Moreover, it sheds new light on the genetic interrelations between pomegranate species worldwide and more accurately defines their genetic nature.

  17. Phylogeography and adaptation genetics of stickleback from the Haida Gwaii archipelago revealed using genome-wide single nucleotide polymorphism genotyping.

    Science.gov (United States)

    Deagle, Bruce E; Jones, Felicity C; Absher, Devin M; Kingsley, David M; Reimchen, Thomas E

    2013-04-01

    Threespine stickleback populations are model systems for studying adaptive evolution and the underlying genetics. In lakes on the Haida Gwaii archipelago (off western Canada), stickleback have undergone a remarkable local radiation and show phenotypic diversity matching that seen throughout the species distribution. To provide a historical context for this radiation, we surveyed genetic variation at >1000 single nucleotide polymorphism (SNP) loci in stickleback from over 100 populations. SNPs included markers evenly distributed throughout genome and candidate SNPs tagging adaptive genomic regions. Based on evenly distributed SNPs, the phylogeographic pattern differs substantially from the disjunct pattern previously observed between two highly divergent mtDNA lineages. The SNP tree instead shows extensive within watershed population clustering and different watersheds separated by short branches deep in the tree. These data are consistent with separate colonizations of most watersheds, despite underlying genetic connections between some independent drainages. This supports previous suppositions that morphological diversity observed between watersheds has been shaped independently, with populations exhibiting complete loss of lateral plates and giant size each occurring in several distinct clades. Throughout the archipelago, we see repeated selection of SNPs tagging candidate freshwater adaptive variants at several genomic regions differentiated between marine-freshwater populations on a global scale (e.g. EDA, Na/K ATPase). In estuarine sites, both marine and freshwater allelic variants were commonly detected. We also found typically marine alleles present in a few freshwater lakes, especially those with completely plated morphology. These results provide a general model for postglacial colonization of freshwater habitat by sticklebacks and illustrate the tremendous potential of genome-wide SNP data sets hold for resolving patterns and processes underlying recent

  18. Mapping meiotic single-strand DNA reveals a new landscape of DNA double-strand breaks in Saccharomyces cerevisiae.

    Directory of Open Access Journals (Sweden)

    Cyril Buhler

    2007-12-01

    Full Text Available DNA double-strand breaks (DSBs, which are formed by the Spo11 protein, initiate meiotic recombination. Previous DSB-mapping studies have used rad50S or sae2Delta mutants, which are defective in break processing, to accumulate Spo11-linked DSBs, and report large (> or = 50 kb "DSB-hot" regions that are separated by "DSB-cold" domains of similar size. Substantial recombination occurs in some DSB-cold regions, suggesting that DSB patterns are not normal in rad50S or sae2Delta mutants. We therefore developed a novel method to map genome-wide, single-strand DNA (ssDNA-associated DSBs that accumulate in processing-capable, repair-defective dmc1Delta and dmc1Delta rad51Delta mutants. DSBs were observed at known hot spots, but also in most previously identified "DSB-cold" regions, including near centromeres and telomeres. Although approximately 40% of the genome is DSB-cold in rad50S mutants, analysis of meiotic ssDNA from dmc1Delta shows that most of these regions have substantial DSB activity. Southern blot assays of DSBs in selected regions in dmc1Delta, rad50S, and wild-type cells confirm these findings. Thus, DSBs are distributed much more uniformly than was previously believed. Comparisons of DSB signals in dmc1, dmc1 rad51, and dmc1 spo11 mutant strains identify Dmc1 as a critical strand-exchange activity genome-wide, and confirm previous conclusions that Spo11-induced lesions initiate all meiotic recombination.

  19. Dynamic micro-organization of P2X7 receptors revealed by PALM based single particle tracking

    Directory of Open Access Journals (Sweden)

    Amulya Nidhi Shrivastava

    2013-11-01

    Full Text Available Adenosine triphosphate (ATP-gated P2X7 receptors (P2X7Rs are members of the purinergic receptor family that are expressed in several cell types including neurons. A high concentration of ATP is required for the channel opening of P2X7Rs compared to other members of this receptor family. Recent work suggests that ATP binding to members of the P2X receptor family determines the diffusion and localization of these receptors on the plasma membrane of neurons. Here, we employed single particle tracking photoactivated localization microscopy (sptPALM to study the diffusion and ATP-dependence of rat P2X7Rs. Dendra2-tagged P2X7Rs were transfected in hippocampal neurons and imaged on proximal dendrites. Our results suggest the presence of two populations of P2X7Rs within the extra-synaptic membrane: a population composed of rapidly diffusing receptors and one stabilized within nanoclusters (~100 nm diameter. P2X7R trajectories were rarely observed at synaptic sites. P2X7R mutations in the ATP-binding site (K64A or the conserved phosphorylation site (K17A resulted in faster- and slower-diffusing receptors, respectively. Furthermore, ATP differentially accelerated wild type and K17A-mutant receptors but not K64A-mutant receptors. Our results indicate that receptor conformation plays a critical role in regulating ATP-mediated changes in P2X7R diffusion and micro-organization.

  20. Dynamic micro-organization of P2X7 receptors revealed by PALM based single particle tracking.

    Science.gov (United States)

    Shrivastava, Amulya N; Rodriguez, Pamela C; Triller, Antoine; Renner, Marianne

    2013-01-01

    Adenosine triphosphate (ATP)-gated P2X7 receptors (P2X7Rs) are members of the purinergic receptor family that are expressed in several cell types including neurons. A high concentration of ATP is required for the channel opening of P2X7Rs compared to other members of this receptor family. Recent work suggests that ATP binding to members of the P2X receptor family determines the diffusion and localization of these receptors on the plasma membrane of neurons. Here, we employed single particle tracking photoactivated localization microscopy (sptPALM) to study the diffusion and ATP-dependence of rat P2X7Rs. Dendra2-tagged P2X7Rs were transfected in hippocampal neurons and imaged on proximal dendrites. Our results suggest the presence of two populations of P2X7Rs within the extra-synaptic membrane: a population composed of rapidly diffusing receptors and one stabilized within nanoclusters (~100 nm diameter). P2X7R trajectories were rarely observed at synaptic sites. P2X7R mutations in the ATP-binding site (K64A) or the conserved phosphorylation site (K17A) resulted in faster- and slower-diffusing receptors, respectively. Furthermore, ATP differentially accelerated wild type and K17A-mutant receptors but not K64A-mutant receptors. Our results indicate that receptor conformation plays a critical role in regulating ATP-mediated changes in P2X7R diffusion and micro-organization.